WO2022216624A1 - Compositions and methods for generating alpha-beta t cells from induced pluripotent stem cells - Google Patents

Compositions and methods for generating alpha-beta t cells from induced pluripotent stem cells Download PDF

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WO2022216624A1
WO2022216624A1 PCT/US2022/023347 US2022023347W WO2022216624A1 WO 2022216624 A1 WO2022216624 A1 WO 2022216624A1 US 2022023347 W US2022023347 W US 2022023347W WO 2022216624 A1 WO2022216624 A1 WO 2022216624A1
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Prior art keywords
cell
ipsc
tcr
cells
seq
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PCT/US2022/023347
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French (fr)
Inventor
Mark WALLET
Katherine SANTOSTEFANO
Brenda SALANTES
Mark MENDONCA
Toshinobu Nishimura
Michael Francis NASO
Buddha GURUNG
Zengrong ZHU
Barry Morse
Luis Borges
Jill Marinari CARTON
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Century Therapeutics, Inc.
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Priority to CA3214473A priority Critical patent/CA3214473A1/en
Priority to EP22723252.7A priority patent/EP4320224A1/en
Priority to AU2022255166A priority patent/AU2022255166A1/en
Priority to CN202280040273.1A priority patent/CN117441010A/en
Priority to JP2023561609A priority patent/JP2024513906A/en
Publication of WO2022216624A1 publication Critical patent/WO2022216624A1/en

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Definitions

  • This application provides genetically engineered induced pluripotent stem cells (iPSCs) and derivative cells thereof expressing a rearranged ab T cell receptor (TCR). Also provided are uses of the iPSCs or derivative cells thereof to express a chimeric antigen receptor for allogenic cell therapy. Further provided are related vectors, polynucleotides, and pharmaceutical compositions.
  • iPSCs genetically engineered induced pluripotent stem cells
  • TCR ab T cell receptor
  • Chimeric antigen receptor (CAR) T (CART) cells have revolutionized cancer therapies by providing a new approach to eliminate malignant cells in an antigen-specific manner.
  • CAR Chimeric antigen receptor
  • Currently approved versions of CART are autologous products wherein the CAR molecule is delivered as a transgene using a lentiviral vector. While efficacious, significant limitations of this method include the duration of manufacturing, the cost of manufacturing, poor T cell health in many cancer patients which renders the cell product inferior, and inability to generate multiple doses for repeat treatments. Some of these limitations are being addressed by development of allogenic methods wherein peripheral blood T cells from a healthy donor are used to manufacture multiple doses of CART as an off-the-shelf product. However, new challenges emerge for this platform.
  • HLA human leukocyte antigens
  • TCRs T cell receptors expressed by the donor T cells are incompatible for the mismatched HLA molecules of the recipient and can thus participate in graft versus host disease, a potentially life-threatening complication of T cell allografts.
  • a trusted TCR is a specific T cell receptor with a reduced likelihood of causing graft versus host disease.
  • TCRs are diverse heterodimeric cell surface receptors that arise during the process of thymic selection during T cell development. The random nature of TCR rearrangement results in mature TCR protein complexes that are capable of recognizing antigens in the context of HLA-mediated antigen presentation.
  • a specific stage of T cell development is dedicated to removal of such ‘ autoreactive ’ T cells. This process is called negative selection.
  • an autoreactive pre-T cell thymocyte
  • thymocyte an autoreactive pre-T cell
  • TCR tumor necrosis factor
  • the diverse T cell pool is purged of any potentially harmful autoreactive T cells.
  • negative selection does not eliminate T cells that might react to antigens/HLA in another individual. This is the fundamental basis for graft versus host disease wherein allogenic T cell grafts include some cells that can recognize the antigen/HLA complexes of the recipient and then attack the recipient cells.
  • TCR sequences have been developed in populations of people. While the vast majority of TCR sequences are so-called ‘private’ sequences (occurring only infrequently in different people), a portion of TCRs found in humans are public (occurring frequently amongst people with a shared HLA or shared infectious agent) (DeWitt et al., Elife. 2018 Aug 28;7:e38358.). Within known public TCRs, there are well-characterized receptors that recognize specific viruses in people with specific HLA-alleles. One of these is a TCR using the TRBV19 gene which recognizes an influenza A epitope in the context of HLA-A*02:01 (DeWitt et al., Elife.
  • TRBV19 TCRs often pair with an alpha TCR chain TRAV27 and recognize the influenza peptide GILGFVFTL (Choo et al., J Virol. 2014 Sep;88(l 8): 10613-23; Chen et al., Cell Rep. 2017 Apr 18;19(3):569-583).
  • Described herein are methods for generating CAR T cells expressing a trusted TCR derived from induced pluripotent stem cells (iPSCs).
  • iPSCs induced pluripotent stem cells
  • a genetically engineered induced pluripotent stem cell or a derivative cell thereof comprises (i) one or more polynucleotides encoding a recombinant rearranged ab T cell receptor (TCR); and (ii) a polynucleotide encoding a chimeric antigen receptor (CAR), wherein the rearranged ab TCR is a public TCR that specifically recognizes a non-human antigen in the context of a specific HLA class I (HLA-I) allele and wherein the rearranged ab TCR supports differentiation of the iPSC to a T cell.
  • TCR recombinant rearranged ab T cell receptor
  • CAR chimeric antigen receptor
  • the rearranged ab TCR enables expansion of the T cell differentiated from the iPSC after mitogenic stimulation.
  • the one or more polynucleotides encoding the recombinant rearranged ab TCR comprise an a TCR variable gene selected from the group consisting of TRAV27 and TRAV13-1; an a TCRjoining gene selected from the group consisting of TRAJ41 and TRAJ37; and an a TCR constant gene TRAC.
  • the one or more polynucleotides encoding the recombinant rearranged ab TCR comprise a b chain variable gene TRBV19; a b chain variable gene selected from the group consisting of TRBJ2-7, TRBJ2-5, and TRBJ2-6; a b chain constant gene selected from the group consisting of TRBC1 and TRBC2.
  • the recombinant rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza- A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
  • the virus is selected from the group consisting of influenza- A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
  • the iPSC is reprogrammed from peripheral blood mononuclear cells (PBMCs), preferably CD34+ hematopoietic stem cells (HSCs) or ab T cells.
  • PBMCs peripheral blood mononuclear cells
  • HSCs hematopoietic stem cells
  • ab T cells ab T cells
  • T cell derived from the iPSC cell according to the application.
  • an induced pluripotent stem cell or a T cell derived therefrom comprising: one or more polynucleotides encoding a rearranged ab T cell receptor (TCR), wherein the rearranged ab TCR is a public TCR that specifically recognizes a non-human antigen in the context of a specific HLA class I (HLA-I) allele and the rearranged ab TCR supports differentiation of the iPSC to the T cell, and an exogenous polynucleotide encoding a chimeric antigen receptor (CAR); and one or more of the following additional features:
  • IL-15 interleukin 15
  • IL-15 receptor an exogenous polynucleotide encoding interleukin 15 (IL-15) and/or IL-15 receptor or a variant or truncation thereof;
  • HLA-E human leukocyte antigen E
  • HLA-G human leukocyte antigen G
  • the rearranged ab TCR is recombinant.
  • the iPSC is reprogrammed from peripheral blood mononuclear cells (PBMCs), preferably CD34+ hematopoietic stem cells (HSCs) or ab T cells.
  • PBMCs peripheral blood mononuclear cells
  • HSCs hematopoietic stem cells
  • ab T cells ab T cells
  • the rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
  • the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
  • the iPSC or T cell comprises an exogenous polynucleotide encoding a human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G).
  • HLA-E human leukocyte antigen E
  • HLA-G human leukocyte antigen G
  • one or more of the exogenous polynucleotides are integrated at one or more loci on the chromosome of the cell selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, HI 1, GAPDH, RUNX1, B2M, TAPI, TAP2, Tapasin,
  • NLRC5 CIITA, RFXANK, CIITA, RFX5, RFXAP, TRAC, TRBCl, TRBC2, RAG1, RAG2, NKG2A, NKG2D, CD38, CIS, CBL-B, SOCS2, PD1, CTLA4, LAG3, TIM3, or TIGIT genes, provided at least one of the exogenous polynucleotides is integrated at a locus of a gene selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes to thereby result in a deletion or reduced expression of the gene.
  • one or more of the exogenous polynucleotides are integrated at the loci of the CIITA, AAVS1 and B2M genes.
  • the iPSC or T cell has a deletion or reduced expression of one or more of B2M or CIITA genes.
  • the rearranged ab TCR comprises an a TCR chain having a CDR3 of the amino acid sequence of SEQ ID NO: 84, and a b TCR chain having a CDR3 of the amino acid sequence of SEQ ID NO: 85.
  • the ab TCR comprises an a TCR chain comprising the amino acid sequence encoded by TRAV27 and TRAJ41 genes, and having the CDR3 of the amino acid sequence of SEQ ID NO: 84, and the b TCR chain comprising the amino acid sequence encoded by TRBV19 and TRBJ2-7 genes, and having the CDR3 of the amino acid sequence of SEQ ID NO: 85.
  • the CAR comprises:
  • the signal peptide is GMCSF signal peptide.
  • the extracellular domain comprises an scFv or VHH derived from an antibody that specifically binds an antigen that is expressed on cancer cells.
  • the hinge region comprises a CD28 hinge region, a CD8 hinge region, or an IgG hinge region.
  • the transmembrane domain comprises a CD28 transmembrane domain or a CD8 transmembrane domain.
  • the intracellular signaling domain is derived from DAP10,
  • DAP 12 Fc epsilon receptor I g chain (FCER1G), FcR b, NKG2D, CD35, CD3c, CD3y, O ⁇ 3z, CD5, CD22, CD226, CD66d, CD79A, or CD79B.
  • the co-stimulatory domain is a co-stimulatory signaling domains are derived from CD28, 41BB, IL2Rb, CD40, 0X40 (CD134), CD80, CD86, CD27, ICOS, NKG2D, DAP 10, DAP 12, or 2B4 (CD244).
  • the CAR comprises:
  • the signal peptide comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 1;
  • the extracellular domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 7;
  • the hinge region comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 22;
  • transmembrane domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 24;
  • the intracellular signaling domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 6;
  • the co-stimulatory domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 20.
  • the mechanism of action of the artificial cell death polypeptide is metabolic, dimerization-inducing or therapeutic monoclonal antibody-mediated.
  • the therapeutic monoclonal antibody mediated artificial cell death polypeptide is an inactivated cell surface protein selected from the group of monoclonal antibody specific epitopes selected from epitopes specifically recognized by ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, polatuzumab vedotin, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimuma
  • the inactivated cell surface protein is a truncated epithelial growth factor (tEGFR) variant.
  • tEGFR truncated epithelial growth factor
  • the tEGFR variant consists of an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 71.
  • the HLA-E comprises an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 66 or the HLA-G comprises an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 69.
  • the exogenous polynucleotide encoding the chimeric antigen receptor (CAR) is integrated at a locus of AAVS1 gene;
  • the exogenous polypeptide encoding the artificial cell death polypeptide is integrated at a locus of CIITA gene;
  • the exogenous polypeptide encoding the human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G) is integrated at a locus of B2M gene; wherein integration of the exogenous polynucleotides deletes or reduces expression of CIITA and B2M.
  • iPSC induced pluripotent stem cell
  • T cell comprising:
  • a polynucleotide encoding a rearranged T cell receptor (TCR) locus comprising a a TCR having the amino acid sequence of SEQ ID NO: 86, and a b TCR having the amino acid sequence of SEQ ID NO: 87; and (iv) optionally, an exogenous polynucleotide encoding a human leukocyte antigen E (HLA-E) having the amino acid sequence of SEQ ID NO: 66; wherein one or more of the exogenous polynucleotides are integrated at loci of AAVS1, CIITA and B2M genes, to thereby delete or reduce expression of CIITA and B2M.
  • TCR rearranged T cell receptor
  • composition comprising the T cell according embodiments of the application.
  • the composition further comprises or is provided or used in combination with, one or more therapeutic agents selected from the group consisting of a peptide, a cytokine, a checkpoint inhibitor, a mitogen, a growth factor, a small RNA, a dsRNA (double stranded RNA), siRNA, oligonucleotide, mononuclear blood cells, a vector comprising one or more polynucleic acids of interest, an antibody, a chemotherapeutic agent or a radioactive moiety, or an immunomodulatory drug (IMiD).
  • one or more therapeutic agents selected from the group consisting of a peptide, a cytokine, a checkpoint inhibitor, a mitogen, a growth factor, a small RNA, a dsRNA (double stranded RNA), siRNA, oligonucleotide, mononuclear blood cells, a vector comprising one or more polynucleic acids of interest, an antibody, a chemotherapeutic agent
  • a method of manufacturing a T cell of the application comprising differentiating an iPSC cell of the application under conditions for cell differentiation to thereby obtain the T cell.
  • the iPSC is obtained by genomic engineering an iPSC, wherein the genomic engineering comprises targeted editing.
  • targeted editing include, but are not limited to, deletion, insertion, or in/del carried out by CRISPR, ZFN, TALEN, homing nuclease, homology recombination, or any other functional variation of these methods.
  • HPC hematopoietic progenitor cell
  • iPSC induced pluripotent stem cell
  • TCR rearranged ab T cell receptor
  • the rearranged ab TCR is a public TCR that specifically recognizes a non-human antigen in the context of a specific HLA class I (HLA-I) allele and the rearranged ab TCR supports differentiation of the iPSC to a T cell, and an exogenous polynucleotide encoding a chimeric antigen receptor (CAR); and one or more of the following additional features:
  • HLA-E human leukocyte antigen E
  • HLA-G human leukocyte antigen G
  • HPC hematopoietic progenitor cell
  • iPSC induced-pluripotent stem cell
  • HPC hematopoietic progenitor cell
  • iPSC induced-pluripotent stem cell
  • HPC hematopoietic progenitor cell
  • culturing the cell in medium comprising recombinant Delta-like protein 4 (DLL4) and recombinant Jagged 2 (JAG2), optionally further comprising a fibronectin protein or fragment thereof;
  • DLL4 Delta-like protein 4
  • JAG2 recombinant Jagged 2
  • the DLL4 and JAG2 proteins are immobilized on a cell culture plate, such as by using poly dopamine in the presence or absence of Protein G coating.
  • DLL4 Delta-like protein 4 variant polypeptide having an amino acid comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 90.
  • iPSC induced-pluripotent stem cell
  • HPC hematopoietic progenitor cell
  • FIGS. 1A-C show schematics of methods of generating ab iT cells using induced pluripotent stem cells (iPSCs) as a source.
  • FIG. 1A shows a method of generating ab T cells using iPSCs derived from mature ab T cells with a known antigen specificity and HLA- restriction collected from a blood sample.
  • FIG. IB shows a method of generating ab iT cells using iPSCs derived from CD34+ hematopoietic stem cells (HSC) collected from a blood sample.
  • FIG. 1C shows a method of generating ab iT cells using iPSCs derived from mature ab T cells collected from a blood sample with TCR of unknown antigen specificity replaced by trusted TCR.
  • FIG. 2 shows iPSC-derived T (iT) yield when hematopoietic progenitor cells (HPCs) are differentiated in DLL4 or DLL4 and JAG2.
  • iT iPSC-derived T
  • FIG. 3 shows iPSC-derived T (iT) cell yield and percent viability of iT cells differentiated from hematopoietic progenitor cells (HPCs) culture with and without interleukin- 15 (IL-15).
  • FIG. 4 shows the percent viability of iPSC-derived T (iT) engineered to express a CD 19 and percent lysis of target cells by iPSC-derived T (iT) engineered to express a CD 19 targeting chimeric antigen receptor (CAR) in iT cells differentiated in DLL4 or DLL4 and JAG2.
  • HPCs hematopoietic progenitor cells
  • IL-15 interleukin- 15
  • FIG. 5 shows iPSC-derived T (iT) cell yield and percent lysis of target cells by iPSC- derived T (iT) engineered to express a CD19 in iT cells differentiated in the anti-CD3 antibodies OKT3 or UCHTl.
  • FIG. 6 is a schematic of a method for differentiating hematopoietic progenitor cells (HPCS) to iPSC-derived T (iT) cells.
  • HPCS hematopoietic progenitor cells
  • FIG. 7 shows graphs of representative FACS results showing cell markers expressed by iPSC-derived ab T (iT) cells after 28 days of differentiation.
  • FIG. 8 shows expression of FMC63 (CD19-specific) CAR on iT cells.
  • CAR-iT cells were left unstained (top) or stained with anti-FMC63 CAR antibody (bottom).
  • FIGs. 9A-B shows antigen-specific killing of B cell lymphoma cells by CAR-iT cells.
  • FIG. 9 A shows antigen-positive Reh lymphoma cells (CD 19-expressing lymphoma line) killing by either CAR-iT cells (black squares) or PBMC -derived CART cells (grey circles).
  • FIG. 9B shows antigen-negative Reh lymphoma cells (CD 19 antigen removed by genetic deletion) by either CAR-iT cells (black squares) or PBMC-derived CART cells (grey circles).
  • FIG. 10 shows a schematic of the alpha TCR chain and beta TCR chain of a public TCR.
  • FIG. 11 shows exemplary HLA-restricted TCR combinations.
  • FIG. 12 shows the percent viability of NALM6 cells expressing a negative control or an influenza peptide (GILGFVFTL) cultured with ab iT cells engineered to express a trusted TCR which targets the influenza peptide at an effector to target ratio of 1 : 1 or 5: 1.
  • GILGFVFTL negative control or an influenza peptide
  • any numerical values such as a concentration or a concentration range described herein, are to be understood as being modified in all instances by the term “about.”
  • a numerical value typically includes ⁇ 10% of the recited value.
  • a concentration of 1 mg/mL includes 0.9 mg/mL to 1.1 mg/mL.
  • a concentration range of 1% to 10% (w/v) includes 0.9% (w/v) to 11% (w/v).
  • the use of a numerical range expressly includes all possible subranges, all individual numerical values within that range, including integers within such ranges and fractions of the values unless the context clearly indicates otherwise.
  • the terms “comprises,” “comprising,” “includes,” “including,” “has,” “having,” “contains” or “containing,” or any other variation thereof, will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers and are intended to be non-exclusive or open-ended.
  • a composition, a mixture, a process, a method, an article, or an apparatus that comprises a list of elements is not necessarily limited to only those elements but can include other elements not expressly listed or inherent to such composition, mixture, process, method, article, or apparatus.
  • “or” refers to an inclusive or and not to an exclusive or. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).
  • the conjunctive term “and/or” between multiple recited elements is understood as encompassing both individual and combined options. For instance, where two elements are conjoined by “and/or,” a first option refers to the applicability of the first element without the second. A second option refers to the applicability of the second element without the first. A third option refers to the applicability of the first and second elements together. Any one of these options is understood to fall within the meaning, and therefore satisfy the requirement of the term “and/or” as used herein. Concurrent applicability of more than one of the options is also understood to fall within the meaning, and therefore satisfy the requirement of the term “and/or.”
  • subject means any animal, preferably a mammal, most preferably a human.
  • mammal encompasses any mammal. Examples of mammals include, but are not limited to, cows, horses, sheep, pigs, cats, dogs, mice, rats, rabbits, guinea pigs, monkeys, humans, etc., more preferably a human.
  • nucleic acids or polypeptide sequences e.g., CAR polypeptides and the CAR polynucleotides that encode them
  • sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection.
  • sequence comparison typically one sequence acts as a reference sequence, to which test sequences are compared.
  • test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated.
  • sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
  • Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat’l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by visual inspection ⁇ see generally, Current Protocols in Molecular Biology, F.M. Ausubel et al, eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1995 Supplement) (Ausubel)).
  • Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always > 0) and N (penalty score for mismatching residues; always ⁇ 0).
  • M forward score for a pair of matching residues; always > 0
  • N penalty score for mismatching residues; always ⁇ 0.
  • a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment.
  • W wordlength
  • E expectation
  • BLOSUM62 scoring matrix see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).
  • the BLAST algorithm In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul,
  • nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
  • a further indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the polypeptide encoded by the second nucleic acid, as described below.
  • a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions.
  • Another indication that two nucleic acid sequences are substantially identical is that the two molecules hybridize to each other under stringent conditions.
  • isolated means a biological component (such as a nucleic acid, peptide, protein, or cell) has been substantially separated, produced apart from, or purified away from other biological components of the organism in which the component naturally occurs, i.e., other chromosomal and extrachromosomal DNA and RNA, proteins, cells, and tissues.
  • Nucleic acids, peptides, proteins, and cells that have been “isolated” thus include nucleic acids, peptides, proteins, and cells purified by standard purification methods and purification methods described herein.
  • isolated nucleic acids, peptides, proteins, and cells can be part of a composition and still be isolated if the composition is not part of the native environment of the nucleic acid, peptide, protein, or cell.
  • the term also embraces nucleic acids, peptides and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.
  • biomolecule refers to a biomolecule that (1) has been removed from its naturally occurring environment, (2) is not associated with all or a portion of another biomolecule in which the biomolecule is found in nature, (3) is operatively linked to another biomolecule which it is not linked to in nature, or (4) does not occur in nature.
  • biomolecule include, e.g., a nucleic acid or a polypeptide.
  • recombinant can be used in reference to cloned DNA isolates, chemically synthesized polynucleotide or polypeptide, or analogs thereof, or polynucleotide or polypeptide, or analogs thereof that are biologically synthesized by heterologous systems, as well as proteins and/or mRNAs encoded by such recombinant nucleic acids.
  • nucleic acid molecule As used herein, the term “polynucleotide,” synonymously referred to as “nucleic acid molecule,” “nucleotides” or “nucleic acids,” refers to any polyribonucleotide or polydeoxyribonucleotide, which can be unmodified RNA or DNA or modified RNA or DNA.
  • Polynucleotides include, without limitation single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that can be single-stranded or, more typically, double-stranded or a mixture of single- and double- stranded regions.
  • polynucleotide refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA.
  • the term polynucleotide also includes DNAs or RNAs containing one or more modified bases and DNAs or RNAs with backbones modified for stability or for other reasons.
  • Modified bases include, for example, tritylated bases and unusual bases such as inosine.
  • polynucleotide embraces chemically, enzymatically or metabolically modified forms of polynucleotides as typically found in nature, as well as the chemical forms of DNA and RNA characteristic of viruses and cells.
  • Polynucleotide also embraces relatively short nucleic acid chains, often referred to as oligonucleotides.
  • a “construct” refers to a macromolecule or complex of molecules comprising a polynucleotide to be delivered to a host cell, either in vitro or in vivo.
  • a “vector,” as used herein refers to any nucleic acid construct capable of directing the delivery or transfer of a foreign genetic material to target cells, where it can be replicated and/or expressed.
  • the term “vector” as used herein comprises the construct to be delivered.
  • a vector can be a linear or a circular molecule.
  • a vector can be integrating or non-integrating.
  • the major types of vectors include, but are not limited to, plasmids, episomal vector, viral vectors, cosmids, and artificial chromosomes.
  • Viral vectors include, but are not limited to, adenovirus vector, adeno-associated virus vector, retrovirus vector, lentivirus vector, Sendai virus vector, and the like.
  • integration it is meant that one or more nucleotides of a construct is stably inserted into the cellular genome, i.e., covalently linked to the nucleic acid sequence within the cell's chromosomal DNA.
  • target integration it is meant that the nucleotide(s) of a construct is inserted into the cell's chromosomal or mitochondrial DNA at a pre-selected site or “integration site”.
  • integration as used herein further refers to a process involving insertion of one or more exogenous sequences or nucleotides of the construct, with or without deletion of an endogenous sequence or nucleotide at the integration site. In the case, where there is a deletion at the insertion site, “integration” can further comprise replacement of the endogenous sequence or a nucleotide that is deleted with the one or more inserted nucleotides.
  • the term “exogenous” is intended to mean that the referenced molecule or the referenced activity is introduced into, or non-native to, the host cell.
  • the molecule can be introduced, for example, by introduction of an encoding nucleic acid into the host genetic material such as by integration into a host chromosome or as non- chromosomal genetic material such as a plasmid. Therefore, the term as it is used in reference to expression of an encoding nucleic acid refers to introduction of the encoding nucleic acid in an expressible form into the cell.
  • the term “endogenous” refers to a referenced molecule or activity that is present in the host cell in its native form. Similarly, the term when used in reference to expression of an encoding nucleic acid refers to expression of an encoding nucleic acid natively contained within the cell and not exogenously introduced.
  • a “gene of interest” or “a polynucleotide sequence of interest” is a DNA sequence that is transcribed into RNA and in some instances translated into a polypeptide in vivo when placed under the control of appropriate regulatory sequences.
  • a gene or polynucleotide of interest can include, but is not limited to, prokaryotic sequences, cDNA from eukaryotic mRNA, genomic DNA sequences from eukaryotic (e.g., mammalian) DNA, and synthetic DNA sequences.
  • a gene of interest may encode an miRNA, an shRNA, a native polypeptide (i.e. a polypeptide found in nature) or fragment thereof; a variant polypeptide (i.e. a mutant of the native polypeptide having less than 100% sequence identity with the native polypeptide) or fragment thereof; an engineered polypeptide or peptide fragment, a therapeutic peptide or polypeptide, an imaging marker, a selectable marker, and the like.
  • “Operably-linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other.
  • a promoter is operably-linked with a coding sequence or functional RNA when it is capable of affecting the expression of that coding sequence or functional RNA (i.e., the coding sequence or functional RNA is under the transcriptional control of the promoter).
  • Coding sequences can be operably- linked to regulatory sequences in sense or antisense orientation.
  • the term encompasses the transcription of a gene into RNA.
  • the term also encompasses translation of RNA into one or more polypeptides, and further encompasses all naturally occurring post- transcriptional and post-translational modifications.
  • the expressed CAR can be within the cytoplasm of a host cell, into the extracellular milieu such as the growth medium of a cell culture or anchored to the cell membrane.
  • peptide can refer to a molecule comprised of amino acids and can be recognized as a protein by those of skill in the art.
  • the conventional one-letter or three-letter code for amino acid residues is used herein.
  • peptide can be used interchangeably herein to refer to polymers of amino acids of any length.
  • the polymer can be linear or branched, it can comprise modified amino acids, and it can be interrupted by non-amino acids.
  • the terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component. Also included within the definition are, for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids, etc.), as well as other modifications known in the art.
  • the peptide sequences described herein are written according to the usual convention whereby the N-terminal region of the peptide is on the left and the C-terminal region is on the right. Although isomeric forms of the amino acids are known, it is the L-form of the amino acid that is represented unless otherwise expressly indicated.
  • engineered immune cell refers to an immune cell, also referred to as an immune effector cell, that has been genetically modified by the addition of exogenous genetic material in the form of DNA or RNA to the total genetic material of the cell.
  • iPSCs Induced Pluripotent Stem Cells (iPSCs) And Immune Effector Cells
  • IPSCs have unlimited self-renewing capacity.
  • Use of iPSCs enables cellular engineering to produce a controlled cell bank of modified cells that can be expanded and differentiated into desired immune effector cells, supplying large amounts of homogeneous allogeneic therapeutic products.
  • iPSCs and derivative cells thereof.
  • the selected genomic modifications provided herein enhance the therapeutic properties of the derivative cells.
  • the derivative cells are functionally improved and suitable for allogeneic off- the-shelf cell therapies following a combination of selective modalities being introduced to the cells at the level of iPSC through genomic engineering. This approach can help to reduce the side effects mediated by CRS/GVHD and prevent long-term autoimmunity while providing excellent efficacy.
  • the engineered iPSC’s hereof are capable of being differentiated into alpha beta T cell immune effector cells.
  • differentiation is the process by which an unspecialized ("uncommitted") or less specialized cell acquires the features of a specialized cell.
  • Specialized cells include, for example, a blood cell or a muscle cell.
  • a differentiated or differentiation- induced cell is one that has taken on a more specialized ("committed") position within the lineage of a cell.
  • embryonic stem cells are a type of pluripotent stem cells that are able to form cells from each of the three germs layers, the ectoderm, the mesoderm, and the endoderm.
  • Pluripotency is a continuum of developmental potencies ranging from the incompletely or partially pluripotent cell (e.g., an epiblast stem cell or EpiSC), which is unable to give rise to a complete organism to the more primitive, more pluripotent cell, which is able to give rise to a complete organism (e.g., an embryonic stem cell).
  • the incompletely or partially pluripotent cell e.g., an epiblast stem cell or EpiSC
  • EpiSC epiblast stem cell
  • a complete organism e.g., an embryonic stem cell
  • induced pluripotent stem cells or, iPSCs, means that the stem cells are produced from differentiated adult, neonatal or fetal cells that have been induced or changed or reprogrammed into cells capable of differentiating into tissues of all three germ or dermal layers: mesoderm, endoderm, and ectoderm.
  • the iPSCs produced do not refer to cells as they are found in nature.
  • reprogramming or “dedifferentiation” refers to a method of increasing the potency of a cell or dedifferentiating the cell to a less differentiated state.
  • a cell that has an increased cell potency has more developmental plasticity (i.e., can differentiate into more cell types) compared to the same cell in the non-reprogrammed state.
  • a reprogrammed cell is one that is in a less differentiated state than the same cell in a non-reprogrammed state.
  • hematopoietic stem and progenitor cells refers to cells which are committed to a hematopoietic lineage but are capable of further hematopoietic differentiation.
  • Hematopoietic stem cells include, for example, multipotent hematopoietic stem cells (hematoblasts), myeloid progenitors, megakaryocyte progenitors, erythrocyte progenitors, and lymphoid progenitors.
  • Hematopoietic stem and progenitor cells are multipotent stem cells that give rise to all the blood cell types including myeloid (monocytes and macrophages, neutrophils, basophils, eosinophils, erythrocytes, megakaryocytes/platelets, dendritic cells), and lymphoid lineages (T cells, B cells, NK cells).
  • myeloid monocytes and macrophages
  • neutrophils neutrophils
  • basophils basophils
  • eosinophils neutrophils
  • eosinophils neutrophils
  • basophils basophils
  • eosinophils neutrophils
  • erythrocytes erythrocytes
  • megakaryocytes/platelets dendritic cells
  • dendritic cells lymphoid lineages
  • CD34+ hematopoietic progenitor cell refers to an HPC that expresses CD34 on its surface.
  • immune cell or “immune effector cell” refers to a cell that is involved in an immune response. Immune response includes, for example, the promotion of an immune effector response. Examples of immune cells include T cells, B cells, natural killer (NK) cells, mast cells, and myeloid-derived phagocytes.
  • NK natural killer
  • T lymphocyte and “T cell” are used interchangeably and refer to a type of white blood cell that completes maturation in the thymus and that has various roles in the immune system.
  • a T cell can have the roles including, e.g., the identification of specific foreign antigens in the body and the activation and deactivation of other immune cells.
  • a T cell can be any T cell, such as a cultured T cell, e.g., a primary T cell, or a T cell from a cultured T cell line, e.g., Jurkat, SupTl, etc., or a T cell obtained from a mammal.
  • the T cell can be CD3+ cells.
  • the T cell can be any type of T cell and can be of any developmental stage, including but not limited to, CD4+/CD8+ double positive T cells, CD4+ helper T cells (e.g., Thl and Th2 cells), CD8+ T cells (e.g., cytotoxic T cells), peripheral blood mononuclear cells (PBMCs), peripheral blood leukocytes (PBLs), tumor infiltrating lymphocytes (TILs), memory T cells, naive T cells, regulator T cells, gamma delta T cells (gd T cells), and the like.
  • helper T cells include cells such as Th3 (Treg), Thl7, Th9, or Tfh cells.
  • T cells such as central memory T cells (Tcm cells), effector memory T cells (Tern cells and TEMRA cells).
  • the T cell can also refer to a genetically engineered T cell, such as a T cell modified to express a T cell receptor (TCR) and/or a chimeric antigen receptor (CAR).
  • TCR T cell receptor
  • CAR chimeric antigen receptor
  • the T cell can also be differentiated from a stem cell or progenitor cell.
  • CD4+ T cells refers to a subset of T cells that express CD4 on their surface and are associated with cell-mediated immune response. They are characterized by the secretion profiles following stimulation, which can include secretion of cytokines such as IFN-gamma, TNF-alpha, IL2, IL4 and IL10. “CD4” are 55-kD glycoproteins originally defined as differentiation antigens on T-lymphocytes, but also found on other cells including monocytes/macrophages. CD4 antigens are members of the immunoglobulin supergene family and are implicated as associative recognition elements in MHC (major histocompatibility complex) class Il-restricted immune responses. On T-lymphocytes they define the helper/inducer subset.
  • CD8+ T cells refers to a subset of T cells which express CD8 on their surface, are MHC class I-restricted, and function as cytotoxic T cells.
  • CD8 molecules are differentiation antigens found on thymocytes and on cytotoxic and suppressor T- lymphocytes. CD8 antigens are members of the immunoglobulin supergene family and are associative recognition elements in major histocompatibility complex class I-restricted interactions.
  • the induced pluripotent stem cell (iPSC) parental cell lines can be generated from peripheral blood mononuclear cells (PBMCs) or T cells using any known method for introducing re-programming factors into non-pluripotent cells using methods known in the art.
  • PBMCs peripheral blood mononuclear cells
  • T cells T cells
  • the so called “Thompson Factors” as described in U.S. Pat. Nos. 8183038, 8268620, 8440461, 9499786, 10,865,381 can be used, or the Yamanaka Factors as described in U.S. Pat. No. 8,952,801 the complete disclosures of which are incorporated herein by reference.
  • Methods include the episomal plasmid-based process as previously described in U.S. Pat. Nos.
  • the reprogramming factors can be in a form of polynucleotides, and thus are introduced to the non-pluripotent cells by vectors such as a retrovirus, a Sendai virus, an adenovirus, an episome, and a mini-circle.
  • the one or more polynucleotides encoding at least one reprogramming factor are introduced by a lentiviral vector.
  • the one or more polynucleotides introduced by an episomal vector are introduced by a Sendai viral vector.
  • the iPSC’s are clonal iPSC’s or are obtained from a pool of iPSCs and the genome edits are introduced by making one or more targeted integration and/or in/del at one or more selected sites.
  • the iPSC’s are obtained from human T cells having antigen specificity and a reconstituted TCR gene (hereinafter, also referred to as "T-iPS” cells or “T-iPSC”) as described in US Pat. Nos. 9206394, and 10787642 hereby incorporated by reference into the present application.
  • FIG. 1A-C show schematics of exemplary methods for generating iPSCs of the application.
  • the term “genetic imprint” refers to genetic or epigenetic information that contributes to preferential therapeutic attributes in a source cell or an iPSC, and is retainable in the source cell derived iPSCs, and/or the iPSC-derived hematopoietic lineage cells.
  • a source cell is a non-pluripotent cell that can be used for generating iPSCs through reprogramming, and the source cell derived iPSCs can be further differentiated to specific cell types including any hematopoietic lineage cells.
  • the source cell derived iPSCs, and differentiated cells therefrom are sometimes collectively called “derived” or “derivative” cells depending on the context.
  • derivative effector cells or derivative T or “iT” cells are cells differentiated from an iPSC, as compared to their primary counterpart obtained from natural/native sources such as peripheral blood, umbilical cord blood, or other donor tissues.
  • the genetic imprint(s) conferring a preferential therapeutic attribute is incorporated into the iPSCs either through reprogramming a selected source cell that is donor-, disease-, or treatment response- specific, or through introducing genetically modified modalities to iPSC using genomic editing.
  • the application provides an induced pluripotent stem cell (iPSC) that comprises one or more polynucleotides encoding a rearranged ab TCR, wherein the rearranged ab TCR is a public TCR that specifically recognizes a non-human antigen in the context of a specific HLA class I (HLA-I) allele and wherein the rearranged ab TCR supports differentiation of the iPSC to a T cell.
  • iPSC induced pluripotent stem cell
  • a T cell receptor is a membrane complex found on the surface of T cells that recognizes antigens specifically. It is a heterodimer consisting of alpha (a) and beta (b) chains or gamma (g) and delta (d) chains. Each of the alpha, beta, gamma and delta chains of a TCR can be a glycoprotein.
  • a TCR generates its diversity in a manner similar to that for antibodies, e g., mainly from genetic recombination of the DNA-encoded segments in individual somatic T cells by somatic V(D)J recombination.
  • the T cell receptor loci are rearranged and expressed stochastically. If both delta and gamma rearrangements produce functional polypeptides, the cell expresses delta and gamma. If not, the cell proceeds to rearrange the beta and alpha loci.
  • TCR genes do not undergo somatic hypermutation.
  • the TCRa gene locus contains variable (V) and joining (J) gene segments (nb and Ib), whereas the TCRb locus contains a D gene segment in addition to Va and Ja segments. Accordingly, the a chain is generated from VJ recombination and the b chain is generated involving VDJ recombination.
  • TCRy chain is generated involving VJ recombination and the TCR5 gene is generated involving VDJ recombination.
  • the gene segments for TCR are flanked by the same recombination signal sequences as are the Ig gene segments, and the same RAG-1 and RAG-2 encoded recombinase and TdT are required for somatic recombination.
  • a “rearranged TCR” is a TCR encoded by a rearranged TCR gene which has undergone a physical rearrangement whereby distant sub-genes are fused together.
  • the human genome possesses four unique TCR gene clusters; alpha (a), beta (b), gamma (g), and delta (d), encoding the TCR alpha, beta, gamma and delta chains, respectively, via rearranged TCR genes.
  • Each chain of the TCR has a variable and a constant region.
  • the variable region contains three hypervariable or complementarity-determining regions (CDRs) and framework residues.
  • CDR3 is mainly responsible for recognizing a processed antigen.
  • the TCR forms a molecular complex with the CD3 complex, which contains a CD3 gamma (g) chain, a CD3 delta (d) chain, two CD3 epsilon (e) chains, and two CD3 zeta (Q chains.
  • Alpha-beta T cell receptors or “ab TCR” are antigen specific T cell receptors essential to the immune response and have one a (alpha) chain and one b (beta) chain. Binding of ab TCR to peptide-major histocompatibility complex (pMHC) initiates TCR-CD3 intracellular activation, recruitment of numerous signaling molecules, and branching and integrating signaling pathways, leading to mobilization of transcription factors that are critical for gene expression and T cell growth and function acquisition. T cells with aB TCRs have specific reactivity to peptides presented via human leukocyte antigen (HLA) system or complex.
  • HLA is the human nomenclature for MHC genes and proteins and can be used interchangeably (e.g. HLA-I is equivocal to MHC-I)
  • HLA-restricted antigen recognition refers to the fact that a T cell can recognize a foreign peptide bound to a self-major histocompatibility complex molecule, but will only respond to the antigen when it is bound to a particular HLA molecule (e.g., HLA- A*0201).
  • HLA- A*0201 HLA- A*0201
  • T cells go through a selection process in the thymus to ensure that the TCR will not recognize HLA molecules presenting self-antigens. The selection process results in developed T cells with specific TCRs that only respond to certain HLA molecules but not others (e.g., non-restricted MHC molecules).
  • a “public TCR” or “trusted TCR” is a TCR that comprises a sequence that occurs in multiple individuals with a certain HLA type. These sequences occur so frequently in people who carry the restricting HLA allele, that they have been proven in nature to be compatible with a vast diversity of HLA-I alleles. Thus, these TCRs fail to recognize non- restricted HLA molecules and are unlikely to participate in graft versus host disease. Public TCRs and methods of identifying them have been described by Choo et al., J Virol. 2014 Sep;88(18): 10613-23; Valkenburg et al., Proc Natl Acad Sci U S A.
  • the T cell receptor alpha locus encodes the T cell receptor alpha chain.
  • the human TRA locus is composed of 54 variable genes (TRAY) genes belonging to 41 subgroups, 61 joining segments (TRAJ), and a unique constant region (TRAC) gene.
  • TRAY variable genes
  • TRAJ 61 joining segments
  • TRAC unique constant region
  • the TRA repertoire comprises 45-47 functional TRAV genes belonging to 33-35 subgroups, 50 functional TRAJ segments, and the unique TRAC gene.
  • a recombination event occurs at the DNA level joining a V gene with a J segment, and the C gene is later joined by splicing at the RNA level.
  • Recombination of different V gene segments with several J segments provides a range of antigen recognition. Additional diversity in antigen recognition is attained by junctional diversity, resulting from the random addition of nucleotides by terminal deoxynucleotidyl transferase.
  • a polynucleotide encoding a a TCR chain comprises a a TCR variable gene selected from the group consisting of TRAV27 and TRAV13-1; an a TCRjoining gene selected from the group consisting of TRAJ41 and TRAJ37; and an a TCR constant gene TRAC.
  • T cell receptor beta locus encodes the T cell receptor beta chain.
  • the human TRB locus is composed of 39-46 functional TRBV genes belonging to 21-23 subgroups, two diversity regions (TRBD), thirteen joining segments (TRBJ), and two constant (TRBC) gene.
  • TRBD two diversity regions
  • TRBJ thirteen joining segments
  • TRBC constant
  • a polynucleotide encoding a b TCR chain comprises a b chain variable gene TRBV19; a b chain variable gene selected from the group consisting of TRBJ2-7, TRBJ2-5, and TRBJ2-6; a b chain constant gene selected from the group consisting of TRBC 1 and TRBC2.
  • the rearranged ab TCR is endogenous to the ab T cell.
  • the rearranged ab TCR is recombinant.
  • the rearranged ab TCR enables increased expansion of the differentiated T cell after mitogenic stimulation than a T cell without the rearranged ab TCR.
  • the rearranged ab TCR binds to an antigen derived from a virus, bacteria, fungi or parasites. In certain embodiments, the rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza- A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
  • EBV Epstein-Barr virus
  • CMV Cytomegalovirus
  • the rearranged ab TCR binds to an influenza peptide comprising the amino acid sequence of SEQ ID NO: 83.
  • the rearranged ab TCR comprises an a TCR chain having a CDR3 of the amino acid sequence of SEQ ID NO: 84, and a b TCR chain having a CDR3 of the amino acid sequence of SEQ ID NO: 85.
  • the ab TCR comprises an a TCR chain comprising the amino acid sequence encoded by TRAV27 and TRAJ41 genes, and having the CDR3 of the amino acid sequence of SEQ ID NO: 84, and the b TCR chain comprising the amino acid sequence encoded by TRBV19 and TRBJ2-7 genes, and having the CDR3 of the amino acid sequence of SEQ ID NO: 85.
  • an iPSC cell comprises (i) one or more polynucleotides encoding rearranged ab T cell receptor (TCR); and (ii) a polynucleotide encoding a chimeric antigen receptor (CAR), such as a CAR targeting a tumor antigen.
  • TCR ab T cell receptor
  • CAR chimeric antigen receptor
  • chimeric antigen receptor refers to a recombinant polypeptide comprising at least an extracellular domain that binds specifically to an antigen or a target, a transmembrane domain and an intracellular signaling domain. Engagement of the extracellular domain of the CAR with the target antigen on the surface of a target cell results in clustering of the CAR and delivers an activation stimulus to the CAR-containing cell. CARs redirect the specificity of immune effector cells and trigger proliferation, cytokine production, phagocytosis and/or production of molecules that can mediate cell death of the target antigenexpressing cell in a major histocompatibility (MHC)-independent manner.
  • MHC major histocompatibility
  • signal peptide refers to a leader sequence at the amino- terminus (N-terminus) of a nascent CAR protein, which co-translationally or post-translationally directs the nascent protein to the endoplasmic reticulum and subsequent surface expression.
  • extracellular antigen binding domain refers to the part of a CAR that is located outside of the cell membrane and is capable of binding to an antigen, target or ligand.
  • hinge region or “hinge domain” refers to the part of a CAR that connects two adjacent domains of the CAR protein, i.e., the extracellular domain and the transmembrane domain of the CAR protein.
  • transmembrane domain refers to the portion of a CAR that extends across the cell membrane and anchors the CAR to cell membrane.
  • intracellular signaling domain refers to the part of a CAR that is located inside of the cell membrane and is capable of transducing an effector signal.
  • the term “stimulatory molecule” refers to a molecule expressed by an immune cell (e.g., T cell) that provides the primary cytoplasmic signaling sequence(s) that regulate primary activation of receptors in a stimulatory way for at least some aspect of the immune cell signaling pathway.
  • Stimulatory molecules comprise two distinct classes of cytoplasmic signaling sequence, those that initiate antigen-dependent primary activation (referred to as “primary signaling domains”), and those that act in an antigen-independent manner to provide a secondary of co-stimulatory signal (referred to as “co-stimulatory signaling domains”).
  • the extracellular domain comprises an antigen binding domain and/or an antigen binding fragment.
  • the antigen binding fragment can, for example, be an antibody or antigen binding fragment thereof that specifically binds a tumor antigen.
  • the antigen binding fragments of the application possess desirable functional properties, including but not limited to high-affinity binding to a tumor antigen.
  • antibody is used in a broad sense and includes immunoglobulin or antibody molecules including human, humanized, composite and chimeric antibodies and antibody fragments that are monoclonal or polyclonal. In general, antibodies are proteins or peptide chains that exhibit binding specificity to a specific antigen. Antibody structures are well known. Immunoglobulins can be assigned to five major classes (i.e., IgA, IgD, IgE, IgG and IgM), depending on the heavy chain constant domain amino acid sequence. IgA and IgG are further sub-classified as the isotypes IgAl, IgA2, IgGl, IgG2, IgG3 and IgG4.
  • the antibodies of the application can be of any of the five major classes or corresponding sub-classes.
  • the antibodies of the application are IgGl, IgG2, IgG3 or IgG4.
  • Antibody light chains of vertebrate species can be assigned to one of two clearly distinct types, namely kappa and lambda, based on the amino acid sequences of their constant domains.
  • the antibodies of the application can contain a kappa or lambda light chain constant domain.
  • the antibodies of the application include heavy and/or light chain constant regions from rat or human antibodies.
  • antibodies contain an antigen-binding region that is made up of a light chain variable region and a heavy chain variable region, each of which contains three domains (i.e., complementarity determining regions 1-3; CDR1, CDR2, and CDR3).
  • the light chain variable region domains are alternatively referred to as LCDR1, LCDR2, and LCDR3, and the heavy chain variable region domains are alternatively referred to as HCDR1, HCDR2, and HCDR3.
  • an “isolated antibody” refers to an antibody which is substantially free of other antibodies having different antigenic specificities (e.g., an isolated antibody that specifically binds to the specific tumor antigen is substantially free of antibodies that do not bind to the tumor antigen). In addition, an isolated antibody is substantially free of other cellular material and/or chemicals.
  • the term “monoclonal antibody” refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that can be present in minor amounts.
  • the monoclonal antibodies of the application can be made by the hybridoma method, phage display technology, single lymphocyte gene cloning technology, or by recombinant DNA methods.
  • the monoclonal antibodies can be produced by a hybridoma which includes a B cell obtained from a transgenic nonhuman animal, such as a transgenic mouse or rat, having a genome comprising a human heavy chain transgene and a light chain transgene.
  • the term “antigen-binding fragment” refers to an antibody fragment such as, for example, a diabody, a Fab, a Fab', a F(ab')2, an Fv fragment, a disulfide stabilized Fv fragment (dsFv), a (dsFv)2, a bispecific dsFv (dsFv-dsFv 1 ), a disulfide stabilized diabody (ds diabody), a single-chain antibody molecule (scFv), a single domain antibody (sdAb), a scFv dimer (bivalent diabody), a multispecific antibody formed from a portion of an antibody comprising one or more CDRs, a camelized single domain antibody, a minibody, a nanobody, a domain antibody, a bivalent domain antibody, a light chain variable domain (VL), a variable domain (VHH) of a camelid antibody, or any other antibody fragment that binds to an antigen-binding
  • an antigen-binding fragment is capable of binding to the same antigen to which the parent antibody or a parent antibody fragment binds.
  • single-chain antibody refers to a conventional single-chain antibody in the field, which comprises a heavy chain variable region and a light chain variable region connected by a short peptide of about 15 to about 20 amino acids (e.g., a linker peptide).
  • single domain antibody refers to a conventional single domain antibody in the field, which comprises a heavy chain variable region and a heavy chain constant region or which comprises only a heavy chain variable region.
  • human antibody refers to an antibody produced by a human or an antibody having an amino acid sequence corresponding to an antibody produced by a human made using any technique known in the art. This definition of a human antibody includes intact or full-length antibodies, fragments thereof, and/or antibodies comprising at least one human heavy and/or light chain polypeptide.
  • humanized antibody refers to a non-human antibody that is modified to increase the sequence homology to that of a human antibody, such that the antigenbinding properties of the antibody are retained, but its antigenicity in the human body is reduced.
  • chimeric antibody refers to an antibody wherein the amino acid sequence of the immunoglobulin molecule is derived from two or more species.
  • the variable region of both the light and heavy chains often corresponds to the variable region of an antibody derived from one species of mammal (e.g., mouse, rat, rabbit, etc.) having the desired specificity, affinity, and capability, while the constant regions correspond to the sequences of an antibody derived from another species of mammal (e.g., human) to avoid eliciting an immune response in that species.
  • multispecific antibody refers to an antibody that comprises a plurality of immunoglobulin variable domain sequences, wherein a first immunoglobulin variable domain sequence of the plurality has binding specificity for a first epitope and a second immunoglobulin variable domain sequence of the plurality has binding specificity for a second epitope.
  • the first and second epitopes are on the same antigen, e.g., the same protein (or subunit of a multimeric protein).
  • the first and second epitopes overlap or substantially overlap.
  • the first and second epitopes do not overlap or do not substantially overlap.
  • the first and second epitopes are on different antigens, e.g., the different proteins (or different subunits of a multimeric protein).
  • a multispecific antibody comprises a third, fourth, or fifth immunoglobulin variable domain.
  • a multispecific antibody is a bispecific antibody molecule, a trispecific antibody molecule, or a tetraspecific antibody molecule.
  • bispecific antibody refers to a multispecific antibody that binds no more than two epitopes or two antigens.
  • a bispecific antibody is characterized by a first immunoglobulin variable domain sequence which has binding specificity for a first epitope and a second immunoglobulin variable domain sequence that has binding specificity for a second epitope.
  • the first and second epitopes are on the same antigen, e.g., the same protein (or subunit of a multimeric protein).
  • the first and second epitopes overlap or substantially overlap.
  • the first and second epitopes are on different antigens, e.g., the different proteins (or different subunits of a multimeric protein).
  • a bispecific antibody comprises a heavy chain variable domain sequence and a light chain variable domain sequence which have binding specificity for a first epitope and a heavy chain variable domain sequence and a light chain variable domain sequence which have binding specificity for a second epitope.
  • a bispecific antibody comprises a half antibody, or fragment thereof, having binding specificity for a first epitope and a half antibody, or fragment thereof, having binding specificity for a second epitope.
  • a bispecific antibody comprises a scFv, or fragment thereof, having binding specificity for a first epitope, and a scFv, or fragment thereof, having binding specificity for a second epitope.
  • a bispecific antibody comprises a VHH having binding specificity for a first epitope, and a VHH having binding specificity for a second epitope.
  • an antigen binding domain or antigen binding fragment that “specifically binds to a tumor antigen” refers to an antigen binding domain or antigen binding fragment that binds a tumor antigen, with a KD of 1 x KG 7 M or less, preferably 1 x 10 8 M or less, more preferably 5> ⁇ 10 9 M or less, H IO -9 M or less, 5xlO 10 M or less, or HIO -10 M or less.
  • KD refers to the dissociation constant, which is obtained from the ratio of Kd to Ka (i.e., Kd/Ka) and is expressed as a molar concentration (M). KD values for antibodies can be determined using methods in the art in view of the present disclosure.
  • the KD of an antigen binding domain or antigen binding fragment can be determined by using surface plasmon resonance, such as by using a biosensor system, e.g., a Biacore® system, or by using bio-layer interferometry technology, such as an Octet RED96 system.
  • a biosensor system e.g., a Biacore® system
  • bio-layer interferometry technology such as an Octet RED96 system.
  • antibodies or antibody fragments suitable for use in the CAR of the present disclosure include, but are not limited to, monoclonal antibodies, bispecific antibodies, multispecific antibodies, chimeric antibodies, polypeptide-Fc fusions, single-chain Fvs (scFv), single chain antibodies, Fab fragments, F(ab') fragments, disulfide-linked Fvs (sdFv), masked antibodies (e g., Probodies®), Small Modular ImmunoPharmaceuticals (“SMIPsTM”), intrabodies, minibodies, single domain antibody variable domains, nanobodies, VHHS, diabodies, tandem diabodies (TandAb®), anti -idiotypic (anti-id) antibodies (including, e.g., anti-id antibodies to antigen-specific TCR), and epitope-binding fragments of any of the above.
  • Antibodies and/or antibody fragments can be derived from murine antibodies, rabbit antibodies, human antibodies, fully humanized antibodies, camelid antibody variable
  • the antigen-binding fragment is an Fab fragment, an Fab 1 fragment, an F(ab')2 fragment, an scFv fragment, an Fv fragment, a dsFv diabody, a VHH, a VNAR, a single-domain antibody (sdAb) or nanobody, a dAb fragment, aFd' fragment, a Fd fragment, a heavy chain variable region, an isolated complementarity determining region (CDR), a diabody, a triabody, or a decabody.
  • the antigen-binding fragment is an scFv fragment.
  • the antigen binding domain of the CAR is a single-domain antibody (sdAb), also known as a nanobody, an antibody fragment consisting of a single monomeric variable antibody domain, including heavy-chain antibodies found in camelids; the so called VHH fragments.
  • sdAb single-domain antibody
  • the antigen binding domain of the CAR is a single-domain antibody (sdAb), also known as a nanobody, an antibody fragment consisting of a single monomeric variable antibody domain, including heavy-chain antibodies found in camelids; the so called VHH fragments.
  • Cartilaginous fishes also have heavy-chain antibodies (IgNAR, 'immunoglobulin new antigen receptor'), from which single-domain antibodies called VNAR fragments can be obtained and these can be used in the invention.
  • An alternative approach is to split the dimeric variable domains from common immunoglobulin G (IgG) from humans or mice into monomers.
  • IgG immunoglobulin G
  • nanobodies derived from light chains have also been shown to bind specifically to target epitopes and can also be employed.
  • Alternative scaffolds to immunoglobulin domains that exhibit similar functional characteristics, such as high-affinity and specific binding of target biomolecules, can also be used in the CARs of the present disclosure.
  • Such scaffolds have been shown to yield molecules with improved characteristics, such as greater stability or reduced immunogenicity.
  • Non-limiting examples of alternative scaffolds that can be used in the CAR of the present disclosure include engineered, tenascin-derived, tenascin type III domain (e.g., CentyrinTM); engineered, gamma-B crystallin-derived scaffold or engineered, ubiquitin-derived scaffold (e.g., Affilins); engineered, fibronectin-derived, 10th fibronectin type III (10Fn3) domain (e.g., monobodies, AdNectinsTM, or AdNexinsTM);; engineered, ankyrin repeat motif containing polypeptide (e.g., DARPinsTM); engineered, low-density -lipoprotein-receptor-derived, A domain (LDLR-A) (e.g., AvimersTM); lipocalin (e.g., anticalins); engineered, protease inhibitor-derived, Kunitz domain (e.g., EET ⁇ - IEAGRP, BP
  • the alternative scaffold is Affilin or Centyrin.
  • the first polypeptide of the CARs of the present disclosure comprises a leader sequence.
  • the leader sequence can be positioned at the N-terminus the extracellular binding domain.
  • the leader sequence can be optionally cleaved from the extracellular binding domain during cellular processing and localization of the CAR to the cellular membrane. Any of various leader sequences known to one of skill in the art can be used as the leader sequence.
  • Non-limiting examples of peptides from which the leader sequence can be derived include granulocyte-macrophage colony-stimulating factor receptor (GMCSFR),
  • the leader sequence is compatible with the secretory pathway of a T cell.
  • the leader sequence is derived from human immunoglobulin heavy chain (HC).
  • the leader sequence is derived from GMCSFR.
  • the GMCSFR leader sequence comprises the amino acid sequence set forth in SEQ ID NO: 1, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 1.
  • the first polypeptide of the CARs of the present disclosure comprise a transmembrane domain, fused in frame between the extracellular binding domain and the cytoplasmic domain.
  • the transmembrane domain can be derived from the protein contributing to the extracellular binding domain, the protein contributing the signaling or co-signaling domain, or by a totally different protein.
  • the transmembrane domain can be selected or modified by amino acid substitution, deletions, or insertions to minimize interactions with other members of the CAR complex.
  • the transmembrane domain can be selected or modified by amino acid substitution, deletions, or insertions to avoid binding of proteins naturally associated with the transmembrane domain.
  • the transmembrane domain includes additional amino acids to allow for flexibility and/or optimal distance between the domains connected to the transmembrane domain.
  • the transmembrane domain can be derived either from a natural or from a synthetic source. Where the source is natural, the domain can be derived from any membrane-bound or transmembrane protein.
  • Non-limiting examples of transmembrane domains of particular use in this disclosure can be derived from (i.e. comprise at least the transmembrane region(s) of) the a, b or z chain of the T cell receptor (TCR), CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD8a, CD9, CD 16, CD22, CD33, CD37, CD40, CD64, CD80, CD86, CD134, CD137, or CD154.
  • TCR T cell receptor
  • the transmembrane domain can be synthetic, in which case it will comprise predominantly hydrophobic residues such as leucine and valine.
  • a triplet of phenylalanine, tryptophan and/or valine can be found at each end of a synthetic transmembrane domain.
  • transmembrane domain of the z, h or FccRly chains which contain a cysteine residue capable of disulfide bonding so that the resulting chimeric protein will be able to form disulfide linked dimers with itself, or with unmodified versions of the z, h or FcsRly chains or related proteins.
  • the transmembrane domain will be selected or modified by amino acid substitution to avoid binding of such domains to the transmembrane domains of the same or different surface membrane proteins to minimize interactions with other members of the receptor complex.
  • transmembrane domain of z, h or FcsRly and -b, MB1 (Iga.), B29 or CD3- g, z, or h in order to retain physical association with other members of the receptor complex.
  • the transmembrane domain is derived from CD8 or CD28.
  • the CD8 transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 23, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 23.
  • the CD28 transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 24, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 24.
  • the first polypeptide of the CAR of the present disclosure comprises a spacer region between the extracellular binding domain and the transmembrane domain, wherein the binding domain, linker, and the transmembrane domain are in frame with each other.
  • spacer region generally means any oligo- or polypeptide that functions to link the binding domain to the transmembrane domain.
  • a spacer region can be used to provide more flexibility and accessibility for the binding domain.
  • a spacer region can comprise up to 300 amino acids, preferably 10 to 100 amino acids and most preferably 25 to 50 amino acids.
  • a spacer region can be derived from all or part of naturally occurring molecules, such as from all or part of the extracellular region of CD8, CD4 or CD28, or from all or part of an antibody constant region.
  • the spacer region can be a synthetic sequence that corresponds to a naturally occurring spacer region sequence, or can be an entirely synthetic spacer region sequence.
  • Non-limiting examples of spacer regions which can be used in accordance to the disclosure include a part of human CD8a chain, partial extracellular domain of CD28, FcyRllla receptor, IgG, IgM, IgA, IgD, IgE, an Ig hinge, or functional fragment thereof.
  • additional linking amino acids are added to the spacer region to ensure that the antigen-binding domain is an optimal distance from the transmembrane domain.
  • the spacer when the spacer is derived from an Ig, the spacer can be mutated to prevent Fc receptor binding.
  • the spacer region comprises a hinge domain.
  • the hinge domain can be derived from CD8a, CD28, or an immunoglobulin (IgG).
  • IgG hinge can be from IgGl, IgG2, IgG3, IgG4, IgMl, IgM2, IgAl, IgA2, IgD, IgE, or a chimera thereof.
  • the hinge domain comprises an immunoglobulin IgG hinge or functional fragment thereof.
  • the IgG hinge is from IgGl, IgG2, IgG3, IgG4, IgMl, IgM2, IgAl, IgA2, IgD, IgE, or a chimera thereof.
  • the hinge domain comprises the CHI, CH2, CH3 and/or hinge region of the immunoglobulin.
  • the hinge domain comprises the core hinge region of the immunoglobulin.
  • core hinge can be used interchangeably with the term “short hinge” (a.k.a. “SH”).
  • Non-limiting examples of suitable hinge domains are the core immunoglobulin hinge regions include EPKSCDKTHTCPPCP (SEQ ID NO: 57) from IgGl, ERKCCVECPPCP (SEQ ID NO: 58) from IgG2, ELKTPLGDTTHTCPRCP(EPKSCDTPPPCPRCP) 3 (SEQ ID NO: 59) from IgG3, and ESKYGPPCPSCP (SEQ ID NO: 60) from IgG4 (see also Wypych et al., JBC 2008 283(23): 16194-16205, which is incorporated herein by reference in its entirety for all purposes).
  • the hinge domain is a fragment of the immunoglobulin hinge.
  • the hinge domain is derived from CD8 or CD28.
  • the CD8 hinge domain comprises the amino acid sequence set forth in SEQ ID NO: 21, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 21.
  • the CD28 hinge domain comprises the amino acid sequence set forth in SEQ ID NO: 22, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 22.
  • the transmembrane domain and/or hinge domain is derived from CD8 or CD28. In some embodiments, both the transmembrane domain and hinge domain are derived from CD8. In some embodiments, both the transmembrane domain and hinge domain are derived from CD28.
  • the first polypeptide of CARs of the present disclosure comprise a cytoplasmic domain, which comprises at least one intracellular signaling domain.
  • cytoplasmic domain also comprises one or more co-stimulatory signaling domains.
  • the cytoplasmic domain is responsible for activation of at least one of the normal effector functions of the host cell (e g., T cell) in which the CAR has been placed in.
  • effector function refers to a specialized function of a cell. Effector function of a T cell, for example, can be cytolytic activity or helper activity including the secretion of cytokines.
  • signaling domain refers to the portion of a protein which transduces the effector function signal and directs the cell to perform a specialized function. While usually the entire signaling domain is present, in many cases it is not necessary to use the entire chain.
  • intracellular signaling domain is thus meant to include any truncated portion of the signaling domain sufficient to transduce the effector function signal.
  • Non-limiting examples of signaling domains which can be used in the CARs of the present disclosure include, e g., signaling domains derived from DAP10, DAP12, Fc epsilon receptor I g chain (FCER1G), FcR b, CD36, CD3a, CD3y, O ⁇ 3z, CD2, CD5, CD22, CD226, CD66d, CD79A, and CD79B.
  • the cytoplasmic domain comprises a O ⁇ 3z signaling domain.
  • the O ⁇ 3z signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 6, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 6.
  • the cytoplasmic domain further comprises one or more costimulatory signaling domains.
  • the one or more co-stimulatory signaling domains are derived from CD28, 4 IBB, IL2Rb, CD40, 0X40 (CD 134), CD80, CD86, CD27, ICOS, NKG2D, DAP 10, DAP 12, 2B4 (CD244), BTLA, CD30, GITR, CD226, CD79A, and HVEM.
  • the co-stimulatory signaling domain is derived from 41BB.
  • the 4 IBB co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 8, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 8.
  • the co-stimulatory signaling domain is derived from IL2Rb .
  • the IL2Rb co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 9, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 9.
  • the co-stimulatory signaling domain is derived from CD40.
  • the CD40 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 10, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 10.
  • the co-stimulatory signaling domain is derived from 0X40.
  • the 0X40 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 11, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 11.
  • the co-stimulatory signaling domain is derived from CD80.
  • the CD80 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 12, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 12.
  • the co-stimulatory signaling domain is derived from CD86.
  • the CD86 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 13, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 13.
  • the co-stimulatory signaling domain is derived from CD27.
  • the CD27 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 14, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 14.
  • the co-stimulatory signaling domain is derived from ICOS.
  • the ICOS co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 15, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 15.
  • the co-stimulatory signaling domain is derived from NKG2D.
  • the NKG2D co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 16, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 16.
  • the co-stimulatory signaling domain is derived from DAPIO.
  • the DAPIO co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 17, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 17.
  • the co-stimulatory signaling domain is derived from DAP 12.
  • the DAP12 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 18, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 18.
  • the co-stimulatory signaling domain is derived from 2B4 (CD244).
  • the 2B4 (CD244) co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 19, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 19.
  • the CAR of the present disclosure comprises one costimulatory signaling domains. In some embodiments, the CAR of the present disclosure comprises two or more costimulatory signaling domains. In certain embodiments, the CAR of the present disclosure comprises two, three, four, five, six or more costimulatory signaling domains. In some embodiments, the signaling domain(s) and costimulatory signaling domain(s) can be placed in any order. In some embodiments, the signaling domain is upstream of the costimulatory signaling domains. In some embodiments, the signaling domain is downstream from the costimulatory signaling domains. In the cases where two or more costimulatory domains are included, the order of the costimulatory signaling domains could be switched.
  • Non-limiting exemplary CAR regions and sequences are provided in Table 1.
  • the antigen-binding domain of the second polypeptide binds to an antigen.
  • the antigen-binding domain of the second polypeptide can bind to more than one antigen or more than one epitope in an antigen.
  • the antigen-binding domain of the second polypeptide can bind to two, three, four, five, six, seven, eight or more antigens.
  • the antigen-binding domain of the second polypeptide can bind to two, three, four, five, six, seven, eight or more epitopes in the same antigen.
  • antigen-binding domain may depend upon the type and number of antigens that define the surface of a target cell.
  • the antigen-binding domain can be chosen to recognize an antigen that acts as a cell surface marker on target cells associated with a particular disease state.
  • the CARs of the present disclosure can be genetically modified to target a tumor antigen of interest by way of engineering a desired antigen-binding domain that specifically binds to an antigen (e.g., on a tumor cell).
  • Non-limiting examples of cell surface markers that can act as targets for the antigen-binding domain in the CAR of the disclosure include those associated with tumor cells or autoimmune diseases.
  • the antigen-binding domain binds to at least one tumor antigen or autoimmune antigen.
  • the antigen-binding domain binds to at least one tumor antigen. In some embodiments, the antigen-binding domain binds to two or more tumor antigens. In some embodiments, the two or more tumor antigens are associated with the same tumor. In some embodiments, the two or more tumor antigens are associated with different tumors.
  • the antigen-binding domain binds to at least one autoimmune antigen. In some embodiments, the antigen-binding domain binds to two or more autoimmune antigens. In some embodiments, the two or more autoimmune antigens are associated with the same autoimmune disease. In some embodiments, the two or more autoimmune antigens are associated with different autoimmune diseases.
  • the tumor antigen is associated with glioblastoma, ovarian cancer, cervical cancer, head and neck cancer, liver cancer, prostate cancer, pancreatic cancer, renal cell carcinoma, bladder cancer, or hematologic malignancy.
  • tumor antigen associated with glioblastoma include HER2, EGFRvIII, EGFR, CD133, PDGFRA, FGFR1, FGFR3, MET, CD70, ROBOland IL13Ra2.
  • tumor antigens associated with ovarian cancer include FOLR1, FSHR, MUC16, MUC1, Mesothelin, CA125, EpCAM, EGFR, PDGFRa, Nectin-4, and B7H4.
  • Non-limiting examples of the tumor antigens associated with cervical cancer or head and neck cancer include GD2, MUC1, Mesothelin, HER2, and EGFR.
  • Non-limiting examples of tumor antigen associated with liver cancer include Claudin 18.2, GPC-3, EpCAM, cMET, and AFP.
  • Non-limiting examples of tumor antigens associated with hematological malignancies include CD22, CD79 (CD79a and/or CD79b), BCMA, GPRC5D, SLAM F7, CD33, CLL1, CD123, and CD70.
  • Non-limiting examples of tumor antigens associated with bladder cancer include Nectin-4 and SLITRK6.
  • antigens that can be targeted by the antigen-binding domain include, but are not limited to, alpha-fetoprotein, A3, antigen specific for A33 antibody, Ba 733, BrE3 -antigen, carbonic anhydrase EX, CD1, CDla, CD3, CD5, CD15, CD16, CD19, CD20, CD21, CD22, CD23, CD25, CD30, CD33, CD38, CD45, CD74, CD79a, CD80, CD123, CD138, colon-specific antigen-p (CSAp), CEA (CEACAM5), CEACAM6, CSAp, EGFR, EGP-I, EGP- 2, Ep-CAM, EphAl, EphA2, EphA3, EphA4, EphA5, EphA6, EphA7, EphA8, EphAlO, EphBl, EphB2, EphB3, EphB4, EphB6, FIt-I, Flt-3, folate receptor, HLA-DR, human chori
  • the antigen targeted by the antigen-binding domain is CD19.
  • the antigen-binding domain comprises an anti-CD19 scFv.
  • the anti-CD 19 scFv comprises a heavy chain variable region (VH) comprising the amino acid sequence set forth in SEQ ID NO: 2, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 2.
  • VH heavy chain variable region
  • the anti-CD 19 scFv comprises a light chain variable region (VL) comprising the amino acid sequence set forth in SEQ ID NO: 4, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 4.
  • VL light chain variable region
  • the anti-CD19 scFv comprises the amino acid sequence set forth in SEQ ID NO: 7, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 7.
  • the antigen is associated with an autoimmune disease or disorder.
  • Such antigens can be derived from cell receptors and cells which produce “self ’-directed antibodies.
  • the antigen is associated with an autoimmune disease or disorder such as Rheumatoid arthritis (RA), multiple sclerosis (MS), Sjogren's syndrome, Systemic lupus erythematosus, sarcoidosis, Type 1 diabetes mellitus, insulin dependent diabetes mellitus (IDDM), autoimmune thyroiditis, reactive arthritis, ankylosing spondylitis, scleroderma, polymyositis, dermatomyositis, psoriasis, vasculitis, Wegener's granulomatosis, Myasthenia gravis, Hashimoto's thyroiditis, Graves' disease, chronic inflammatory demyelinating polyneuropathy, Guillain-Barre syndrome, Crohn's disease or ulcerative colitis.
  • RA Rheumatoid arthritis
  • autoimmune antigens that can be targeted by the CAR disclosed herein include but are not limited to platelet antigens, myelin protein antigen, Sm antigens in snRNPs, islet cell antigen, Rheumatoid factor, and anticitrullinated protein citrullinated proteins and peptides such as CCP-1, CCP-2 (cyclical citrullinated peptides), fibrinogen, fibrin, vimentin, fillaggrin, collagen I and II peptides, alpha-enolase, translation initiation factor 4G1, perinuclear factor, keratin, Sa (cytoskeletal protein vimentin), components of articular cartilage such as collagen II, IX, and XI, circulating serum proteins such as RFs (IgG, IgM), fibrinogen, plasminogen, ferritin, nuclear components such as RA33/hnRNP A2, Sm, eukaryotic trasnlation elogation factor 1 alpha 1, stress
  • the scFv fragment used in the CAR of the present disclosure can include a linker between the VH and VL domains.
  • the linker can be a peptide linker and can include any naturally occurring amino acid. Exemplary amino acids that can be included into the linker are Gly, Ser Pro, Thr, Glu, Lys, Arg, He, Leu, His and The.
  • the linker should have a length that is adequate to link the VH and the VL in such a way that they form the correct conformation relative to one another so that they retain the desired activity, such as binding to an antigen.
  • the linker can be about 5-50 amino acids long. In some embodiments, the linker is about 10-40 amino acids long.
  • the linker is about 10-35 amino acids long. In some embodiments, the linker is about 10-30 amino acids long. In some embodiments, the linker is about 10-25 amino acids long. In some embodiments, the linker is about 10-20 amino acids long. In some embodiments, the linker is about 15-20 amino acids long.
  • Exemplary linkers that can be used are Gly rich linkers, Gly and Ser containing linkers, Gly and Ala containing linkers, Ala and Ser containing linkers, and other flexible linkers.
  • the linker is a Whitlow linker.
  • the Whitlow linker comprises the amino acid sequence set forth in SEQ ID NO: 3, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 3.
  • the linker is a (GrS)3 linker.
  • the (G4S)3 linker comprises the amino acid sequence set forth in SEQ ID NO: 25, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 25.
  • linker sequences can include portions of immunoglobulin hinge area, CL or CHI derived from any immunoglobulin heavy or light chain isotype.
  • Exemplary linkers that can be used include any of SEQ ID NOs: 26-56 in Table 1. Additional linkers are described for example in Int. Pat. Publ. No. W02019/060695, incorporated by reference herein in its entirety. III. Artificial Cell Death Polypeptide Safety Switch
  • an iPSC cell or a derivative cell thereof comprises an exogenous polynucleotide encoding an artificial cell death polypeptide.
  • an artificial cell death polypeptide refers to an engineered protein designed to prevent potential toxicity or otherwise adverse effects of a cell therapy.
  • the artificial cell death polypeptide could mediate induction of apoptosis, inhibition of protein synthesis, DNA replication, growth arrest, transcriptional and post-transcriptional genetic regulation and/or antibody -mediated depletion.
  • the artificial cell death polypeptide is activated by an exogenous molecule, e.g. an antibody, anti-viral drug, or radioisotopic conjugate drugs, that when activated, triggers apoptosis and/or cell death of a therapeutic cell.
  • the mechanism of action of the artificial cell death polypeptide is metabolic, dimerization-inducing or therapeutic monoclonal antibody-mediated.
  • artificial cell death polypeptide is an inactivated cell surface receptor that comprises an epitope specifically recognized by an antibody, particularly a monoclonal antibody, which is also referred to herein as a monoclonal antibody-specific epitope.
  • an antibody particularly a monoclonal antibody, which is also referred to herein as a monoclonal antibody-specific epitope.
  • the inactivated cell surface receptor When expressed by iPSCs or derivative cells thereof, the inactivated cell surface receptor is signaling inactive or significantly impaired, but can still be specifically recognized by an antibody.
  • the specific binding of the antibody to the inactivated cell surface receptor enables the elimination of the iPSCs or derivative cells thereof by ADCC and/or ADCP mechanisms, as well as, direct killing with antibody drug conjugates with toxins or radionuclides.
  • the inactivated cell surface receptor comprises an epitope that is selected from epitopes specifically recognized by an antibody, including but not limited to, ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, polatuzumab vedotin, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimumab, belimumab, canakinumab, den
  • Epidermal growth factor receptor also known as EGFR, ErbBl and HER1
  • EGFR epidermal growth factor receptor
  • ErbBl ErbBl
  • HER1 is a cell- surface receptor for members of the epidermal growth factor family of extracellular ligands.
  • truncated EGFR “tEGFR,” “short EGFR” or “sEGFR” refers to an inactive EGFR variant that lacks the EGF-binding domains and the intracellular signaling domains of the EGFR.
  • An exemplary tEGFR variant contains residues 322-333 of domain 2, all of domains 3 and 4 and the transmembrane domain of the native EGFR sequence containing the cetuximab binding epitope.
  • tEGFR variant on the cell surface enables cell elimination by an antibody that specifically binds to the tEGFR, such as cetuximab (Erbitux®), as needed. Due to the absence of the EGF-binding domains and intracellular signaling domains, tEGFR is inactive when expressed by iPSCs or derivative cell thereof.
  • An exemplary inactivated cell surface receptor of the application comprises a tEGFR variant.
  • expression of the inactivated cell surface receptor in an engineered immune cell expressing a chimeric antigen receptor (CAR) induces cell suicide of the engineered immune cell when the cell is contacted with an anti-EGFR antibody.
  • CAR chimeric antigen receptor
  • a subject who has previously received an engineered immune cell of the present disclosure that comprises a heterologous polynucleotide encoding an inactivated cell surface receptor comprising a tEGFR variant can be administered an anti-EGFR antibody in an amount effective to ablate in the subject the previously administered engineered immune cell.
  • the anti-EGFR antibody is cetuximab, matuzumab, necitumumab or panitumumab, preferably the anti-EGFR antibody is cetuximab.
  • the tEGFR variant comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 71, preferably the amino acid sequence of SEQ ID NO: 71.
  • the inactivated cell surface receptor comprises one or more epitopes of CD79b, such as an epitope specifically recognized by polatuzumab vedotin.
  • the CD79b epitope comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 78, preferably the amino acid sequence of SEQ ID NO: 78.
  • the inactivated cell surface receptor comprises one or more epitopes of CD20, such as an epitope specifically recognized by rituximab.
  • the CD20 epitope comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 80, preferably the amino acid sequence of SEQ ID NO: 80.
  • the inactivated cell surface receptor comprises one or more epitopes of Her 2 receptor or ErbB, such as an epitope specifically recognized by trastuzumab.
  • the monoclonal antibody-specific epitope comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 82, preferably the amino acid sequence of SEQ ID NO: 82.
  • the inactivated cell surface receptor further comprises a cytokine.
  • an inactivated cell surface receptor further comprises a hinge domain.
  • the hinge domain is derived from CD8.
  • the CD8 hinge domain comprises the amino acid sequence set forth in SEQ ID NO: 21, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 21.
  • an inactivated cell surface receptor further comprises a transmembrane domain.
  • the transmembrane domain is derived from CD8.
  • the CD8 transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 23, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 23.
  • an inactivated cell surface receptor comprises one or more epitopes specifically recognized by an antibody in its extracellular domain, a transmembrane region and a cytoplasmic domain.
  • the inactivated cell surface receptor further comprises a hinge region between the epitope(s) and the transmembrane region.
  • the inactivated cell surface receptor comprises more than one epitopes specifically recognized by an antibody, the epitopes can have the same or different amino acid sequences, and the epitopes can be linked together via a peptide linker, such as a flexible peptide linker have the sequence of (GGGGS)n, wherein n is an integer of 1-8 (SEQ ID NO: 25).
  • the inactivated cell surface receptor further comprises a cytokine.
  • the cytokine is in the cytoplasmic domain of the inactivated cell surface receptor.
  • the cytokine is operably linked to the epitope(s) specifically recognized by an antibody, directly or indirectly, via an autoprotease peptide sequence, such as those described herein.
  • the cytokine is indirectly linked to the epitope(s) by connecting to the transmembrane region via the autoprotease peptide sequence.
  • the artificial cell death polypeptide is a viral enzyme that is recognized by an antiviral drug.
  • the viral enzyme is a herpes simplex virus thymidine kinase (HSV-tk).
  • HSV-tk comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 96, preferably the amino acid sequence of SEQ ID NO: 96.
  • This enzyme phosphorylates the nontoxic prodrug ganciclovir, which then becomes phosphorylated by endogenous kinases to GCV-triphosphate, causing chain termination and single-strand breaks upon incorporation into DNA, thereby killing dividing cells.
  • expression of the viral enzyme in an engineered immune cell expressing a chimeric antigen receptor (CAR) induces cell death of the engineered immune cell when the cell is contacted with an antiviral drug.
  • the antiviral drug is ganciclovir.
  • the artificial cell death polypeptide comprises an antigen targeted by a small molecule compound.
  • the antigen is a truncated prostate-specific membrane antigen (PSMA) polypeptide as described in Inti. Pat. Applications WO2015143029A1 and WO2018187791A1, the disclosures of which are incorporated by reference into the present application in entirety.
  • the prostate-specific membrane antigen (PSMA) polypeptide comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 97, preferably the amino acid sequence of SEQ ID NO: 97.
  • expression of truncated PSMA in an engineered immune cell expressing a chimeric antigen receptor (CAR) induces cell death of the engineered immune cell when the cell is contacted with a radioisotopic conjugate drug that binds to PSMA via a small peptide.
  • PSMA- targeting compounds are described in W02010/108125, the disclosure of which is incorporated herein by reference.
  • the artificial cell death polypeptide comprises a herpes simplex virus thymidine kinase (HSV-tk) fused to a prostate-specific membrane antigen (PSMA) polypeptide via a linker.
  • the linker comprises an amino acid sequence of SEQ ID NO: 48.
  • the artificial cell death polypeptide comprises an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 98, preferably the amino acid sequence of SEQ ID NO: 98.
  • the artificial cell death polypeptide comprises a herpes simplex virus thymidine kinase (HSV-tk) and a prostate-specific membrane antigen (PSMA) polypeptide operably linked by an autoprotease peptide sequence.
  • the autoprotease peptide is a thosea asigna virus 2A (T2A) peptide.
  • the artificial cell death polypeptide comprises an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 99, preferably the amino acid sequence of SEQ ID NO: 99.
  • the artificial polypeptide comprises a prostate-specific membrane antigen (PSMA) polypeptide and a cluster of differentiation 24 (CD24) polypeptide operably linked by an autoprotease peptide sequence.
  • the autoprotease peptide is a thosea asigna virus 2A (T2A) peptide.
  • the artificial cell death polypeptide comprises an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 100, preferably the amino acid sequence of SEQ ID NO: 100.
  • MHC I and/or MHC II knock-out and/or knock down can be incorporated in the cells for use in “allogeneic” cell therapies, in which cells are harvested from a subject, modified to knock-out or knock-down, e.g., disrupt, B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP gene expression, and then returned to a different subject.
  • Knocking out or knocking down the B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes as described herein can: (1) prevent GvH response; (2) prevent HvG response; and/or (3) improve T cell safety and efficacy.
  • a presently disclosed invention comprises independently knocking out and/or knocking down one or more genes selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes in a T cell.
  • a presently disclosed method comprises independently knocking out and/or knocking down two genes selected from the group consisting B2M, TAP 1, TAP 2, Tapasin, RFXANK, CUT A, RFX5 and RFXAP genes in a T cell, in particular, B2M and CIITA to achieve class I and II HLA disruption.
  • an iPSC or derivative cell thereof of the application can be further modified by introducing an exogenous polynucleotide encoding one or more proteins related to immune evasion, such as non-classical HLA class I proteins (e.g., HLA-E and HLA-G).
  • HLA-E and HLA-G non-classical HLA class I proteins
  • disruption of the B2M gene eliminates surface expression of all MHC class I molecules, leaving cells vulnerable to lysis by NK cells through the “missing self’ response.
  • Exogenous HLA-E expression can lead to resistance to NK-mediated lysis (Gornalusse et ah, Nat Biotechnol. 2017; 35(8): 765-772).
  • the iPSC or derivative cell thereof comprises an exogenous polypeptide encoding at least one of a human leukocyte antigen E (HLA-E) and human leukocyte antigen G (HLA-G).
  • HLA-E comprises an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 65, preferably the amino acid sequence of SEQ ID NO: 65.
  • the HLA-G comprises an amino acid sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 68, preferably SEQ ID NO: 68.
  • the exogenous polynucleotide encodes a polypeptide comprising a signal peptide operably linked to a mature B2M protein that is fused to an HLA-E via a linker.
  • the exogenous polypeptide comprises an amino acid sequence at least sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 66.
  • the exogenous polynucleotide encodes a polypeptide comprising a signal peptide operably linked to a mature B2M protein that is fused to an HLA-G via a linker.
  • the exogenous polypeptide comprises an amino acid sequence at least sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 69.
  • a cell of the application further comprises an exogenous polynucleotide encoding interleukin 15 (IL-15) and/or interleukin (IL-15) receptor or a variant or truncation thereof.
  • Interleukin- 15 or “IL-15” refers to a cytokine that regulates T and NK cell activation and proliferation.
  • a “functional portion” (“biologically active portion”) of IL-15 refers to a portion of IL-15 that retains one or more functions of full length or mature IL-15. Such functions include the promotion of NK cell survival, regulation of NK cell and T cell activation and proliferation as well as the support of NK cell development from hematopoietic stem cells.
  • the sequence of a variety of IL-15 molecules are known in the art.
  • the IL-15 is a wild-type IL-15.
  • the IL-15 is a human IL-15.
  • the cell of the application further comprises an exogenous polynucleotide encoding a non-naturally occurring variant of FcyRIII (CD 16), for example, hnCD16 (see, e.g., Zhu et ah, Blood 2017, 130:4452, the contents of which are incorporated herein in their entirety by reference).
  • hnCD16a refers to a high affinity, non-cleavable variant of CD 16 (a low-affinity Fey receptor involved in antibody- dependent cellular cytotoxicity (ADCC).
  • CD16 is cleaved during ADCC by proteases, whereas the hnCD16 CAR does not undergo this cleavage and thus sustains an ADCC signal longer.
  • the hnCD 16 is as disclosed in Blood 2016 128:3363, the entire contents of which is expressly incorporated herein by reference.
  • a cell of the application further comprises an exogenous polynucleotide encoding interleukin 12 (IL-12) or interleukin 21 (IL-21) or a variant thereof.
  • IL-12 interleukin 12
  • IL-21 interleukin 21
  • a cell of the application further comprises an exogenous polynucleotide encoding leukocyte surface antigen cluster of differentiation CD47 (CD47) as an NK inhibitory modality to overcome host-versus-graft immunoreactivity for allogeneic applications.
  • CD47 also sometimes referred to as "integrin associated protein” (LAP) refers to a transmembrane protein that in humans is encoded by the CD47gene.
  • CD47 belongs to the immunoglobulin superfamily, partners with membrane integrins, and also binds the ligands thrombospondin- 1 (TSP-1) and signal-regulatory protein alpha (SIRPa).
  • CD47 acts as a signal to macrophages that allows CD47-expressing cells to escape macrophage attack. See, e.g., Deuse-T, et ah, Nature Biotechnology 201937: 252-258, the entire contents of which are incorporated herein by reference.
  • a cell of the application further comprises an exogeneous polynucleotide encoding a constitutively active IL-7 receptor or variant thereof.
  • IL-7 has a critical role in the development and maturation of T cells. It promotes the generation of naive and central memory T cell subsets and regulates their homeostasis. It has previously been reported that IL-7 prolonged the survival time of tumor-specific T cells in vivo. Cancer Medicine. 2014;3(3):550— 554. In previous studies, it has been reported that a constitutively activated IL-7 receptor (C7R) could result in IL-7 signaling in the absence of a ligand or with the existence of gamma chain (yc) of a coreceptor.
  • C7R constitutively activated IL-7 receptor
  • a cell of the application further comprises an exogenous polynucleotide encoding one or more imaging or reporter proteins, such as PSMA or HSV-tk.
  • the cell can contain an exogeneous polynucleotide encoding prostate-specific membrane antigen (PSMA) as an imaging reporter in accordance with the disclosures of WO2015/ 143029 and WO2018/187791, the disclosures of which are incorporated herein by reference.
  • PSMA prostate-specific membrane antigen
  • the genomic editing at one or more selected sites can comprise insertions of one or more exogenous polynucleotides encoding other additional artificial cell death polypeptides proteins, targeting modalities, receptors, signaling molecules, transcription factors, pharmaceutically active proteins and peptides, drug target candidates, or proteins promoting engraftment, trafficking, homing, viability, self-renewal, persistence, and/or survival of the genome-engineered iPSCs or derivative cells thereof.
  • the exogenous polynucleotides for insertion are operatively linked to (1) one or more exogenous promoters comprising CMV, EFla, PGK, CAG, UBC, or other constitutive, inducible, temporal-, tissue-, or cell type-specific promoters; or (2) one or more endogenous promoters comprised in the selected sites comprising AAVS1, CCR5, ROSA26, collagen, HTRP, HI, beta-2 microglobulin, GAPDH, TCR or RUNX1, or other locus meeting the criteria of a genome safe harbor.
  • exogenous promoters comprising CMV, EFla, PGK, CAG, UBC, or other constitutive, inducible, temporal-, tissue-, or cell type-specific promoters
  • endogenous promoters comprised in the selected sites comprising AAVS1, CCR5, ROSA26, collagen, HTRP, HI, beta-2 microglobulin, GAPDH, TCR or RUNX1, or other locus
  • the genome-engineered iPSCs generated using the above method comprise one or more different exogenous polynucleotides encoding proteins comprising caspase, thymidine kinase, cytosine deaminase, B-cell CD20, ErbB2 or CD79b wherein when the genome-engineered iPSCs comprise two or more suicide genes, the suicide genes are integrated in different safe harbor locus comprising AAVS1, CCR5, ROSA26, collagen, HTRP, Hll, HU, beta-2 microglobulin, GAPDH, TCR or RUNX1.
  • exogenous polynucleotides encoding proteins can include those encoding PET reporters, homeostatic cytokines, and inhibitory checkpoint inhibitory proteins such as PD1, PD-L1, and CTLA4 as well as proteins that target the CD47/signal regulatory protein alpha (SIRPa) axis .
  • the genome-engineered iPSCs generated using the method provided herein comprise in/del at one or more endogenous genes associated with targeting modality, receptors, signaling molecules, transcription factors, drug target candidates, immune response regulation and modulation, or proteins suppressing engraftment, trafficking, homing, viability, self-renewal, persistence, and/or survival of the iPSCs or derivative cells thereof.
  • the modified ab T cells can exhibit one or more edits in their genome that results in a loss-of-function in a target gene.
  • a loss-of-function of a target gene is characterized by a decrease in the expression of a target gene based on a genomic modification, e.g., an RNA- guided nuclease-mediated cut in the target gene that results in an inactivation, or in diminished expression or function, of the encoded gene product.
  • genes that can be targeted for loss of function include B2M, PD-1, CISH, CIITA, HLA class II histocompatibility alpha chain genes (e g HLA-DQA1, HLA-DRA, HLA-DPA1, HLA-DMA- HLA-DQA2 and or HLA- DOA), HLA Class II histocompatabilty beta chain genes (e.g.
  • HLA-DMB HLA-DOB, HLA- DPB1, HLA-DQB1, HLA-DQB2, HLA-DQB3, HLA-DRBl, HLADRB3, HLA-DRB4, and/or HLA-DRB5)
  • CD32B CTLA4, NKG2A, BIM, CCR5,CCR7, CD96, CDK8, CXCR3, EP4 (PGE2 RECEPTOR), Fas, GITR, IL1R8, KIRDLl, KIR2DL1-3, LAG3, SOCS genes, Sortilin, TIM3, TRAC, RAG1, RAG2 and NLRC5.
  • the modified cells of the application can exhibit any of the edits described, as well as any combination of such edits described.
  • one or more of the exogenous polynucleotides are integrated at one or more loci on the chromosome of an iPSC.
  • Genome editing, or genomic editing, or genetic editing, as used interchangeably herein, is a type of genetic engineering in which DNA is inserted, deleted, and/or replaced in the genome of a targeted cell.
  • Targeted genome editing (interchangeable with “targeted genomic editing” or “targeted genetic editing”) enables insertion, deletion, and/or substitution at pre-selected sites in the genome.
  • targeted integration referring to a process involving insertion of one or more exogenous sequences at pre-selected sites in the genome, with or without deletion of an endogenous sequence at the insertion site.
  • Targeted editing can be achieved either through a nuclease-independent approach, or through a nuclease-dependent approach.
  • nuclease-independent targeted editing approach homologous recombination is guided by homologous sequences flanking an exogenous polynucleotide to be inserted, through the enzymatic machinery of the host cell.
  • targeted editing could be achieved with higher frequency through specific introduction of double strand breaks (DSBs) by specific rare-cutting endonucleases.
  • DSBs double strand breaks
  • Such nuclease-dependent targeted editing utilizes DNA repair mechanisms including non-homologous end joining (NHEJ), which occurs in response to DSBs. Without a donor vector containing exogenous genetic material, the NHEJ often leads to random insertions or deletions (in/dels) of a small number of endogenous nucleotides.
  • NHEJ non-homologous end joining
  • the exogenous genetic material can be introduced into the genome during homology directed repair (HDR) by homologous recombination, resulting in a “targeted integration.”
  • HDR homology directed repair
  • DSBs Available endonucleases capable of introducing specific and targeted DSBs include, but not limited to, zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and, RNA-guided CRISPR (Clustered Regular Interspaced Short Palindromic Repeats) systems. Additionally, DICE (dual integrase cassette exchange) system utilizing phiC31 and Bxbl integrases is also a promising tool for targeted integration.
  • ZFN zinc-finger nucleases
  • TALEN transcription activator-like effector nucleases
  • CRISPR Clustered Regular Interspaced Short Palindromic Repeats
  • ZFNs are targeted nucleases comprising a nuclease fused to a zinc finger DNA binding domain.
  • a “zinc finger DNA binding domain” or “ZFBD” it is meant a polypeptide domain that binds DNA in a sequence-specific manner through one or more zinc fingers.
  • a zinc finger is a domain of about 30 amino acids within the zinc finger binding domain whose structure is stabilized through coordination of a zinc ion. Examples of zinc fingers include, but not limited to, C2H2 zinc fingers, C3H zinc fingers, and C4 zinc fingers.
  • a “designed” zinc finger domain is a domain not occurring in nature whose design/composition results principally from rational criteria, e.g., application of substitution rules and computerized algorithms for processing information in a database storing information of existing ZFP designs and binding data. See, for example, U.S. Pat. Nos. 6,140,081; 6,453,242; and 6,534,261; see also WO 98/53058; WO 98/53059; WO 98/53060; WO 02/016536 and WO 03/016496.
  • a “selected” zinc finger domain is a domain not found in nature whose production results primarily from an empirical process such as phage display, interaction trap or hybrid selection. ZFNs are described in greater detail in U.S. Pat. No.
  • a TALEN is a targeted nuclease comprising a nuclease fused to a TAL effector DNA binding domain.
  • transcription activator-like effector DNA binding domain By “transcription activator-like effector DNA binding domain”, “TAL effector DNA binding domain”, or “TALE DNA binding domain” it is meant the polypeptide domain of TAL effector proteins that is responsible for binding of the TAL effector protein to DNA.
  • TAL effector proteins are secreted by plant pathogens of the genus Xanthomonas during infection. These proteins enter the nucleus of the plant cell, bind effector-specific DNA sequences via their DNA binding domain, and activate gene transcription at these sequences via their transactivation domains.
  • TAL effector DNA binding domain specificity depends on an effector-variable number of imperfect 34 amino acid repeats, which comprise polymorphisms at select repeat positions called repeat variable-diresidues (RVD).
  • RVD repeat variable-diresidues
  • TALENs are described in greater detail in U.S. Patent Application No. 2011/0145940, which is herein incorporated by reference.
  • the most recognized example of a TALEN in the art is a fusion polypeptide of the Fokl nuclease to a TAL effector DNA binding domain.
  • targeted nucleases suitable for the present application include, but not limited to Spol 1, Bxbl, phiC3 1, R4, PhiBTl, and Wp/SPBc/TP901-l, whether used individually or in combination.
  • targeted nucleases include naturally occurring and recombinant nucleases; CRISPR related nucleases from families including cas, cpf, cse, csy, csn, csd, cst, csh, csa, csm, and cmr; restriction endonucleases; meganucleases; homing endonucleases, and the like.
  • CRISPR/Cas9 requires two major components: (1) a Cas9 endonuclease and (2) the crRNA-tracrRNA complex.
  • the two components When co-expressed, the two components form a complex that is recruited to a target DNA sequence comprising PAM and a seeding region near PAM.
  • the crRNA and tracrRNA can be combined to form a chimeric guide RNA (gRNA) to guide Cas9 to target selected sequences.
  • gRNA chimeric guide RNA
  • These two components can then be delivered to mammalian cells via transfection or transduction.
  • gRNA chimeric guide RNA
  • CRISPR/Cpfl comprises two major components: (1) a CPfl endonuclease and (2) a crRNA.
  • the two components form a ribobnucleoprotein (RNP) complex that is recruited to a target DNA sequence comprising PAM and a seeding region near PAM.
  • the crRNA can be combined to form a chimeric guide RNA (gRNA) to guide Cpfl to target selected sequences.
  • MAD7 is an engineered Casl2a variant originating from the bacterium E bacterium rectale that has a preference for 5'-TTTN-3' and 5'-CTTN-3' PAM sites and does not require a tracrRNA. See, for example, PCT Publication No. 2018/236548, the disclosure of which is incorporated herein by reference.
  • DICE mediated insertion uses a pair of recombinases, for example, phiC31 and Bxbl, to provide unidirectional integration of an exogenous DNA that is tightly restricted to each enzymes’ own small attB and attP recognition sites. Because these target att sites are not naturally present in mammalian genomes, they must be first introduced into the genome, at the desired integration site. See, for example, U.S. Application Publication No. 2015/0140665, the disclosure of which is incorporated herein by reference.
  • One aspect of the present application provides a construct comprising one or more exogenous polynucleotides for targeted genome integration.
  • the construct further comprises a pair of homologous arm specific to a desired integration site, and the method of targeted integration comprises introducing the construct to cells to enable site specific homologous recombination by the cell host enzymatic machinery.
  • the method of targeted integration in a cell comprises introducing a construct comprising one or more exogenous polynucleotides to the cell, and introducing a ZFN expression cassette comprising a DNA-binding domain specific to a desired integration site to the cell to enable a ZFN-mediated insertion.
  • the method of targeted integration in a cell comprises introducing a construct comprising one or more exogenous polynucleotides to the cell, and introducing a TALEN expression cassette comprising a DNA-binding domain specific to a desired integration site to the cell to enable a TALEN-mediated insertion.
  • the method of targeted integration in a cell comprises introducing a construct comprising one or more exogenous polynucleotides to the cell, introducing a Cpfl expression cassette, and a gRNA comprising a guide sequence specific to a desired integration site to the cell to enable a Cpfl -mediated insertion.
  • the method of targeted integration in a cell comprises introducing a construct comprising one or more exogenous polynucleotides to the cell, introducing a Cas9 expression cassette, and a gRNA comprising a guide sequence specific to a desired integration site to the cell to enable a Cas9-mediated insertion.
  • the method of targeted integration in a cell comprises introducing a construct comprising one or more att sites of a pair of DICE recombinases to a desired integration site in the cell, introducing a construct comprising one or more exogenous polynucleotides to the cell, and introducing an expression cassette for DICE recombinases, to enable DICE-mediated targeted integration.
  • Sites for targeted integration include, but are not limited to, genomic safe harbors, which are intragenic or extragenic regions of the human genome that, theoretically, are able to accommodate predictable expression of newly integrated DNA without adverse effects on the host cell or organism.
  • the genome safe harbor for the targeted integration is one or more loci of genes selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, HU, GAPDH, TCR and RUNX1 genes.
  • the site for targeted integration is selected for deletion or reduced expression of an endogenous gene at the insertion site.
  • the term “deletion” with respect to expression of a gene refers to any genetic modification that abolishes the expression of the gene. Examples of “deletion” of expression of a gene include, e.g., a removal or deletion of a DNA sequence of the gene, an insertion of an exogenous polynucleotide sequence at a locus of the gene, and one or more substitutions within the gene, which abolishes the expression of the gene.
  • MHC deficient including MHC-class I deficient, or MHC-class II deficient, or both, refers to cells that either lack, or no longer maintain, or have reduced level of surface expression of a complete MHC complex comprising a MHC class I protein heterodimer and/or a MHC class II heterodimer, such that the diminished or reduced level is less than the level naturally detectable by other cells or by synthetic methods.
  • MHC class I deficiency can be achieved by functional deletion of any region of the MHC class I locus (chromosome 6p21), or deletion or reducing the expression level of one or more MHC class-I associated genes including, not being limited to, beta-2 microglobulin (B2M) gene, TAP 1 gene, TAP 2 gene and Tapasin genes.
  • B2M gene encodes a common subunit essential for cell surface expression of all MHC class I heterodimers.
  • B2M null cells are MHC-I deficient.
  • MHC class II deficiency can be achieved by functional deletion or reduction of MHC-II associated genes including, not being limited to, RFXANK, CUT A, RFX5 and RFXAP.
  • CIITA is a transcriptional coactivator, functioning through activation of the transcription factor RFX5 required for class II protein expression.
  • CIITA null cells are MHC-II deficient.
  • one or more of the exogenous polynucleotides are integrated at one or more loci of genes selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes to thereby delete or reduce the expression of the gene(s) with the integration.
  • genes for target deletion include, but are not limited to, recombination-activating genes 1 and 2 (RAG1 and RAG2).
  • RAG1 and RAG2 encode parts of a protein complex that initiate V(D)J recombination by introducing double-strand breaks at the border between a recombination signal sequence (RSS) and a coding segment. Deletion or reducing the expression level of the RAG1/RAG2 genes prevents additional TCR rearrangement in the cell, thus preventing unexpected generation of auto-reactive TCR (Minagawa et al., Cell Stem Cell. 2018 Dec 6;23(6):850-858).
  • the exogenous polynucleotides are integrated at one or more loci on the chromosome of the cell, preferably the one or more loci are of genes selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, HI 1, GAPDH, RUNX1, B2M, TAPI, TAP2, Tapasin, NLRC5, CIITA, RFXANK, CIITA, RFX5, RFXAP, TRAC, TRBCl, TRBC2, RAG1, RAG2, NKG2A, NKG2D, CD38, CIS, CBL-B, SOCS2, PD1, CTLA4, LAG3, TIM3, or TIGIT genes, provided at least one of the one or more loci is of a MHC gene, such as a gene selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes.
  • a MHC gene such as a
  • the one or more exogenous polynucleotides are integrated at a locus of an MHC class-I associated gene, such as a beta-2 microglobulin (B2M) gene, TAP 1 gene, TAP 2 gene or Tapasin gene; and at a locus of an MHC-II associated gene, such as a RFXANK, CUT A, RFX5, RFXAP, or CIITA gene; and optionally further at a locus of a safe harbor gene selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, Hll, GAPDH, TCR and RUNX1 genes. More preferably, the one or more of the exogenous polynucleotides are integrated at the loci of CIITA, AAVS1 and B2M genes.
  • B2M beta-2 microglobulin
  • the exogenous polynucleotide encoding the chimeric antigen receptor (CAR) is integrated at a locus of AAVS1 gene;
  • the exogenous polypeptide encoding the artificial cell death polypeptide is integrated at a locus of CIITA gene;
  • the exogenous polypeptide encoding the human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G) is integrated at a locus of B2M gene; wherein integrations of the exogenous polynucleotides delete or reduce expression of CIITA and B2M genes.
  • the invention relates to a cell derived from differentiation of an iPSC of the application, a derivative cell.
  • a derivative cell As described above, the genomic edits introduced into the iPSC cell are retained in the derivative cell.
  • the derivative cell is a T cell.
  • the derivative cell is a CD34+ hematopoietic progenitor cell (HPC).
  • the application provides a CD34+ hematopoietic progenitor cell (HPC) derived from an induced pluripotent stem cell (iPSC) comprising: one or more polynucleotides encoding a rearranged ab T cell receptor (TCR), wherein the rearranged ab TCR is restricted for recognition of a non-human peptide in the context of a specific HLA class I (HLA-I) allele, and an exogenous polynucleotide encoding a chimeric antigen receptor (CAR); and one or more of the following additional features: and one or more of the following additional features:
  • HLA-E human leukocyte antigen E
  • HLA-G human leukocyte antigen G
  • the application provides a T cell comprising one or more polynucleotides encoding a rearranged ab T cell receptor (TCR), wherein the rearranged ab TCR is restricted for recognition of a non-human peptide in the context of a specific HLA class I (HLA-I) allele, and an exogenous polynucleotide encoding a chimeric antigen receptor (CAR); and one or more of the following additional features:
  • the rearranged ab TCR enables increased expansion of the differentiated T cell after mitogenic stimulation than a T cell without the rearranged ab TCR.
  • the iPSC is reprogrammed from a ab T cell and the rearranged ab TCR is endogenous to the ab T cell.
  • the ab TCR is recombinant.
  • the iPSC is reprogrammed from peripheral blood mononuclear cells (PBMCs), preferably CD34+ hematopoietic stem cells (HSCs) or ab T cells.
  • PBMCs peripheral blood mononuclear cells
  • HSCs hematopoietic stem cells
  • ab T cells ab T cells
  • the rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
  • the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
  • the one or more polynucleotides encoding the rearranged ab TCR comprise an a TCR variable gene selected from the group consisting of TRAV27 and TRAV13-1; an a TCRjoining gene selected from the group consisting of TRAJ41 and TRAJ37; and an a TCR constant gene TRAC.
  • the one or more polynucleotides encoding the rearranged ab TCR comprise a b chain variable gene TRBV19; a b chain variable gene selected from the group consisting of TRBJ2-7, TRBJ2-5, and TRBJ2-6; a b chain constant gene selected from the group consisting of TRBCl and TRBC2.
  • the recombinant rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
  • virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
  • the CD34+ or T cell comprises an exogenous polynucleotide encoding a human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G).
  • HLA-E human leukocyte antigen E
  • HLA-G human leukocyte antigen G
  • one or more of the exogenous polynucleotides are integrated at one or more loci on the chromosome of the cell selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, HI 1, GAPDH, RUNX1, B2M, TAPI, TAP2, Tapasin, NLRC5, CIITA, RFXANK, CIITA, RFX5, RFXAP, TRAC, TRBCl, TRBC2, RAG1, RAG2, NKG2A, NKG2D, CD38, CIS, CBL-B, SOCS2, PD1, CTLA4, LAG3, TIM3, or TIGIT genes, provided at least one of the exogenous polynucleotides is integrated at a locus of a gene selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes to thereby result in a deletion or reduced expression of the exogenous poly
  • the exogenous polynucleotide encoding the chimeric antigen receptor (CAR) is integrated at a locus of AAVS1 gene; the exogenous polypeptide encoding the artificial cell death polypeptide is integrated at a locus of CIITA gene; and the exogenous polypeptide encoding the human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G) is integrated at a locus of B2M gene; wherein integration of the exogenous polynucleotides deletes or reduces expression of CIITA and B2M.
  • CAR chimeric antigen receptor
  • a T cell comprising: (i) an exogenous polynucleotide encoding a chimeric antigen receptor (CAR) having the amino acid sequence of SEQ ID NO: 61; (ii) an exogenous polynucleotide encoding an artificial cell death polypeptide comprising an apoptosis- inducing domain having the amino acid sequence of SEQ ID NO: 71; (iii) a polynucleotide encoding a rearranged T cell receptor (TCR) locus comprising a a TCR having the amino acid sequence of SEQ ID NO: 86, and a b TCR having the amino acid sequence of SEQ ID NO: 87; and (iv) optionally, an exogenous polynucleotide encoding a human leukocyte antigen E (HLA- E) having the amino acid sequence of SEQ ID NO: 66; wherein one or more of the exogenous polynucleotides are integrated at loci of
  • An iPSC of the application can be differentiated by any method known in the art. Exemplary methods are described in US8372642, US8574179, US10100282, US10865381, , W02010/099539, W02012/109208, WO2017/070333, W02017/070337, WO2018/067836, WO2018/195175, W02020/061256, WO2017/179720, W02016/010148, and WO2018/048828, each of which are herein incorporated by reference in its entirety.
  • the differentiation protocol can use feeder cells or can be feeder-free.
  • feeder cells are terms describing cells of one type that are co-cultured with cells of a second type to provide an environment in which the cells of the second type can grow, expand, or differentiate, as the feeder cells provide stimulation, growth factors and nutrients for the support of the second cell type.
  • Notch signaling plays a key role in driving precursor cells towards a T cell fate.
  • the Notch family proteins DLL1, DLL4, and Jag2 expressed by stromal cells in the thymus
  • Notchl expressed by early thymocytes.
  • the application also provides a method of differentiating CD34+ hematopoietic progenitor cell (HPC) comprising a polynucleotide encoding a rearranged TCR, such as an induced-pluripotent stem cell (iPSC)-derived CD34+ HPC comprising a polynucleotide encoding a rearranged TCR, to a T cell, the method comprising culturing the CD34+ HPC in a medium comprising Delta-like protein 4 (DLL4) and Jagged 2 (JAG2), optionally further comprising a fibronectin protein or fragment thereof, SCF, FLT3L, TPO, and/or IL-7.
  • HPC hematopoietic progenitor cell
  • iPSC induced-pluripotent stem cell
  • JAG2 Jagged 2
  • the DLL4 and JAG2 proteins are immobilized on a cell culture plate, for example, using poly dopamine in the presence or absence of Protein G coating.
  • the cells are cultured in the medium comprising DLL4 and JAG2 for about 21 to about 35 days, such as 21 days, 28 35 days, or any number of days in between.
  • the recombinant DLL4 is a variant DLL4.
  • Non-limiting exemplary DLL4 variants and sequences are provided in Table 2.
  • the method further comprises culturing the cells in a medium comprising one or more cytokines selected from the group consisting of interleukin-2 (IL-2), IL- 7, and EL-15.
  • IL-2 interleukin-2
  • IL-7 interleukin-7
  • IL-15 extracellular Domain
  • the method comprises culturing the cells in medium comprising IL-2, IL-7 and IL-15.
  • the IL-2, IL-7 and IL-15 are added to the medium on day 21 of differentiation.
  • the method further comprises culturing the cells in medium comprising an anti-CD3 antibody.
  • the anti-CD3 antibody is immobilized on a cell culture plate, for example, direct absorption onto plastic materials such as polystyrene.
  • Non-limiting examples of anti-CD3 antibodies are OKT3 and UCHT1 as described in as described in Rung et al, Science. 1979 Oct 19;206(4416):347-9 and Callard et ak, Clin Exp Immunol. 1981 Mar;43(3):497-505, respectively, the disclosures of which are herein incorporated by reference.
  • the anti-CD3 antibody is OKT3.
  • the anti-CD3 antibody is UCHT1.
  • iPSC induced-pluripotent stem cell
  • HPC hematopoietic progenitor cell
  • the cell is cultured in the medium comprising DLL4 and JAG2 for about 21 to about 35 days, such as 21 days, 28 days, 35 days, or any number of days in between.
  • the cell is cultured in the medium comprising DLL4 and JAG2 from day 0 to about day 21 of differentiation.
  • the cell is cultured in medium comprising IL-2, IL-7, and IL-15 from day 21 to about day 28 of differentiation.
  • the cell is cultured in medium comprising an anti-CD3 antibody, such as OKT3 or UCHT1, day 21 to about day 28 of differentiation.
  • the cell is cultured in medium comprising IL-2, IL-7, and IL-15, and an anti-CD3 antibody, such as OKT3 or UCHT1, from day 21 to about day 28 of differentiation.
  • an anti-CD3 antibody such as OKT3 or UCHT1
  • the invention in another general aspect, relates to an isolated nucleic acid encoding a chimeric antigen receptor (CAR) useful for an invention according to embodiments of the application.
  • CAR chimeric antigen receptor
  • the coding sequence of a CAR can be changed (e.g., replaced, deleted, inserted, etc.) without changing the amino acid sequence of the protein. Accordingly, it will be understood by those skilled in the art that nucleic acid sequences encoding CARs of the application can be altered without changing the amino acid sequences of the proteins.
  • the isolated nucleic acid encodes a CAR targeting CD 19.
  • the isolated nucleic acid encoding the CAR comprises a polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 62, preferably the polynucleotide sequence of SEQ ID NO: 62.
  • the application provides a vector comprising a polynucleotide sequence encoding a CAR useful for an invention according to embodiments of the application.
  • Any vector known to those skilled in the art in view of the present disclosure can be used, such as a plasmid, a cosmid, a phage vector or a viral vector.
  • the vector is a recombinant expression vector such as a plasmid.
  • the vector can include any element to establish a conventional function of an expression vector, for example, a promoter, ribosome binding element, terminator, enhancer, selection marker, and origin of replication.
  • the promoter can be a constitutive, inducible, or repressible promoter.
  • a number of expression vectors capable of delivering nucleic acids to a cell are known in the art and can be used herein for production of a CAR in the cell.
  • Conventional cloning techniques or artificial gene synthesis can be used to generate a recombinant expression vector according to embodiments of the application.
  • the application provides vectors for targeted integration of a CAR useful for an invention according to embodiments of the application.
  • the vector comprises an exogenous polynucleotide having, in the 5’ to 3’ order, (a) a promoter; (b) a polynucleotide sequence encoding a CAR according to an embodiment of the application; and (c) a terminator/polyadenylation signal.
  • the promoter is a CAG promoter.
  • the CAG promoter comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 63.
  • Other promoters can also be used, examples of which include, but are not limited to, EFla, UBC, CMV, SV40, PGK1, and human beta actin.
  • the terminator/ polyadenylation signal is a SV40 signal.
  • the SV40 signal comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 64.
  • Other terminator sequences can also be used, examples of which include, but are not limited to, BGH, hGH, and PGK.
  • the polynucleotide sequence encoding a CAR comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 62.
  • the vector further comprises a left homology arm and a right homology arm flanking the exogenous polynucleotide.
  • left homology arm and right homology arm refers to a pair of nucleic acid sequences that flank an exogenous polynucleotide and facilitate the integration of the exogenous polynucleotide into a specified chromosomal locus. Sequences of the left and right arm homology arms can be designed based on the integration site of interest. In some embodiment, the left or right arm homology arm is homologous to the left or right side sequence of the integration site.
  • the left homology arm comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 80.
  • the right homology arm comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 81.
  • the vector comprises a polynucleotide sequence at least 85%, such as at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 82, preferably the polynucleotide sequence of SEQ ID NO:
  • the invention relates to an isolated nucleic acid encoding an inactivated cell surface receptor useful for an invention according to embodiments of the application.
  • the coding sequence of an inactivated cell surface receptor can be changed (e.g., replaced, deleted, inserted, etc.) without changing the amino acid sequence of the protein.
  • nucleic acid sequences encoding an inactivated cell surface receptor of the application can be altered without changing the amino acid sequences of the proteins.
  • an isolated nucleic acid encodes any inactivated cell surface receptor described herein, such as that comprises a monoclonal antibody-specific epitope, and a cytokine, wherein the monoclonal antibody-specific epitope and the cytokine are operably linked by an autoprotease peptide sequence.
  • the isolated nucleic acid encodes an inactivated cell surface receptor comprising an epitope specifically recognized by an antibody, such as ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, polatuzumab vedotin, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimumab, belimumab, canakinumab, denosuma
  • an antibody
  • the isolated nucleic acid encodes an inactivated cell surface receptor having a truncated epithelial growth factor (tEGFR) variant.
  • the inactivated cell surface receptor comprises an epitope specifically recognized by cetuximab, matuzumab, necitumumab or panitumumab, preferably cetuximab.
  • the isolated nucleic acid encodes an inactivated cell surface receptor having one or more epitopes of CD79b, such as an epitope specifically recognized by polatuzumab vedotin. In certain embodiments, the isolated nucleic acid encodes an inactivated cell surface receptor having one or more epitopes of CD20, such as an epitope specifically recognized by rituximab.
  • the isolated nucleic acid encodes an inactivated cell surface receptor having one or more epitopes of Her 2 receptor, such as an epitope specifically recognized by trastuzumab
  • the autoprotease peptide sequence is porcine tesehovirus-1 2A
  • the truncated epithelial growth factor (tEGFR) variant consists of an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 71.
  • the monoclonal antibody-specific epitope specifically recognized by polatuzumab vedotin consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 74.
  • the monoclonal antibody-specific epitope specifically recognized by rituximab consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 75.
  • the monoclonal antibody-specific epitope specifically recognized by trastuzumab consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 76.
  • the autoprotease peptide has an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 72.
  • the application provides a vector comprising a polynucleotide sequence encoding an inactivated cell surface receptor useful for an invention according to embodiments of the application.
  • Any vector known to those skilled in the art in view of the present disclosure can be used, such as a plasmid, a cosmid, a phage vector or a viral vector.
  • the vector is a recombinant expression vector such as a plasmid.
  • the vector can include any element to establish a conventional function of an expression vector, for example, a promoter, ribosome binding element, terminator, enhancer, selection marker, and origin of replication.
  • the promoter can be a constitutive, inducible, or repressible promoter.
  • a number of expression vectors capable of delivering nucleic acids to a cell are known in the art and can be used herein for production of an inactivated cell surface receptor in the cell.
  • Conventional cloning techniques or artificial gene synthesis can be used to generate a recombinant expression vector according to embodiments of the application.
  • the application provides a vector for targeted integration of an inactivated cell surface receptor useful for an invention according to embodiments of the application.
  • the vector comprises an exogenous polynucleotide having, in the 5’ to 3’ order, (a) a promoter; (b) a polynucleotide sequence encoding an inactivated cell surface receptor, such as an inactivated cell surface receptor comprising a truncated epithelial growth factor (tEGFR) variant.
  • tEGFR truncated epithelial growth factor
  • the promoter is a CAG promoter.
  • the CAG promoter comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 63.
  • Other promoters can also be used, examples of which include, but are not limited to, EFla, UBC, CMV, SV40, PGK1, and human beta actin.
  • the terminator/polyadenylation signal is a SV40 signal.
  • the SV40 signal comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 64.
  • Other terminator sequences can also be used, examples of which include, but are not limited to BGH, hGH, and PGK.
  • the vector further comprises a left homology arm and a right homology arm flanking the exogenous polynucleotide.
  • the invention relates to an isolated nucleic acid encoding an HLA construct useful for an invention according to embodiments of the application.
  • the coding sequence of an HLA construct can be changed (e.g., replaced, deleted, inserted, etc.) without changing the amino acid sequence of the protein.
  • nucleic acid sequences encoding an HL A construct of the application can be altered without changing the amino acid sequences of the proteins.
  • the isolated nucleic acid encodes an HLA construct comprising a signal peptide, such as an HLA-G signal peptide, operably linked to an HLA coding sequence, such as a coding sequence of a mature B2M, and/or a mature HLA-E.
  • the HLA coding sequence encodes the HLA-G and B2M, which are operably linked by a 4X GGGGS linker, and/or the B2M and HLA-E, which are operably linked by a 3X GGGGS linker.
  • the isolated nucleic acid encoding the HLA construct comprises a polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 67, preferably the polynucleotide sequence of SEQ ID NO: 67.
  • the isolated nucleic acid encoding the HLA construct comprises a polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 70, preferably the polynucleotide sequence of SEQ ID NO: 70.
  • the application provides a vector comprising a polynucleotide sequence encoding a HLA construct useful for an invention according to embodiments of the application.
  • Any vector known to those skilled in the art in view of the present disclosure can be used, such as a plasmid, a cosmid, a phage vector or a viral vector.
  • the vector is a recombinant expression vector such as a plasmid.
  • the vector can include any element to establish a conventional function of an expression vector, for example, a promoter, ribosome binding element, terminator, enhancer, selection marker, and origin of replication.
  • the promoter can be a constitutive, inducible, or repressible promoter.
  • a number of expression vectors capable of delivering nucleic acids to a cell are known in the art and can be used herein for production of a HLA construct in the cell.
  • Conventional cloning techniques or artificial gene synthesis can be used to generate a recombinant expression vector according to embodiments of the application.
  • the application provides vectors for targeted integration of a HLA construct useful for an invention according to embodiments of the application.
  • the vector comprises an exogenous polynucleotide having, in the 5’ to 3’ order, (a) a promoter; (b) a polynucleotide sequence encoding an HLA construct; and (c) a terminator/polyadenylation signal.
  • the promoter is a CAG promoter.
  • the CAG promoter comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 63.
  • Other promoters can also be used, examples of which include, but are not limited to, EFla, UBC, CMV, SV40, PGK1, and human beta actin.
  • the terminator/ polyadenylation signal is a SV40 signal.
  • the SV40 signal comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 64.
  • Other terminator sequences can also be used, examples of which include, but are not limited to BGH, hGH, and PGK
  • a polynucleotide sequence encoding a HLA construct comprises a signal peptide, such as a HLA-G signal peptide, a mature B2M, and a mature HLA-E, wherein the HLA-G and B2M are operably linked by a 4X GGGGS linker (SEQ ID NO: 31) and the B2M transgene and HLA-E are operably linked by a 3X GGGGS linker (SEQ ID NO: 25).
  • the HLA construct comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 67, preferably the polynucleotide sequence of SEQ ID NO: 67.
  • the HLA construct comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 70, preferably the polynucleotide sequence of SEQ ID NO: 70.
  • the vector further comprises a left homology arm and a right homology arm flanking the exogenous polynucleotide.
  • the left homology arm comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 77.
  • the right homology arm comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 78.
  • the vector comprises a polynucleotide sequence at least 85%, such as at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 79, preferably the polynucleotide sequence of SEQ ID NO: 79.
  • the application provides a host cell comprising a vector of the application and/or an isolated nucleic acid encoding a construct of the application.
  • Any host cell known to those skilled in the art in view of the present disclosure can be used for recombinant expression of exogenous polynucleotides of the application.
  • the recombinant expression vector is transformed into host cells by conventional methods such as chemical transfection, heat shock, or electroporation, where it is stably integrated into the host cell genome such that the recombinant nucleic acid is effectively expressed.
  • host cells include, for example, recombinant cells containing a vector or isolated nucleic acid of the application useful for the production of a vector or construct of interest; or an engineered iPSC or derivative cell thereof containing one or more isolated nucleic acids of the application, preferably integrated at one or more chromosomal loci.
  • a host cell of an isolated nucleic acid of the application can also be an immune effector cell, such as a T cell, comprising the one or more isolated nucleic acids of the application.
  • the immune effector cell can be obtained by differentiation of an engineered iPSC of the application. Any suitable method in the art can be used for the differentiation in view of the present disclosure.
  • the immune effector cell can also be obtained transfecting an immune effector cell with one or more isolated nucleic acids of the application.
  • the application provides a composition comprising an isolated polynucleotide of the application, a host cell and/or an iPSC or derivative cell thereof of the application.
  • the composition further comprises one or more therapeutic agents selected from the group consisting of a peptide, a cytokine, a checkpoint inhibitor, a mitogen, a growth factor, a small RNA, a dsRNA (double stranded RNA), siRNA, oligonucleotide, mononuclear blood cells, , a vector comprising one or more polynucleic acids of interest, an antibody, a chemotherapeutic agent or a radioactive moiety, or an immunomodulatory drug (IMiD).
  • a therapeutic agents selected from the group consisting of a peptide, a cytokine, a checkpoint inhibitor, a mitogen, a growth factor, a small RNA, a dsRNA (double stranded RNA), siRNA, oligonucleotide, mononuclear blood cells, , a vector comprising one or more polynucleic acids of interest, an antibody, a chemotherapeutic agent or a radioactive mo
  • the composition is a pharmaceutical composition comprising an isolated polynucleotide of the application, a host cell and/or an iPSC or derivative cell thereof of the application and a pharmaceutically acceptable carrier.
  • pharmaceutical composition means a product comprising an isolated polynucleotide of the application, an isolated polypeptide of the application, a host cell of the application, and/or an iPSC or derivative cell thereof of the application together with a pharmaceutically acceptable carrier.
  • Polynucleotides, polypeptides, host cells, and/or iPSCs or derivative cells thereof of the application and compositions comprising them are also useful in the manufacture of a medicament for therapeutic applications mentioned herein.
  • the term “carrier” refers to any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containing vesicle, microsphere, liposomal encapsulation, or other material well known in the art for use in pharmaceutical formulations. It will be understood that the characteristics of the carrier, excipient or diluent will depend on the route of administration for a particular application.
  • the term “pharmaceutically acceptable carrier” refers to a non-toxic material that does not interfere with the effectiveness of a composition described herein or the biological activity of a composition described herein. According to particular embodiments, in view of the present disclosure, any pharmaceutically acceptable carrier suitable for use in a polynucleotide, polypeptide, host cell, and/or iPSC or derivative cell thereof can be used.
  • Non-limiting examples of additional ingredients include: buffers, diluents, solvents, tonicity regulating agents, preservatives, stabilizers, and chelating agents.
  • One or more pharmaceutically acceptable carrier can be used in formulating the pharmaceutical compositions of the application.
  • the application provides a method of treating a disease or a condition in a subject in need thereof.
  • the methods comprise administering to the subject in need thereof a therapeutically effective amount of cells of the application and/or a composition of the application.
  • the disease or condition is cancer.
  • the cancer can, for example, be a solid or a liquid cancer.
  • the cancer can, for example, be selected from the group consisting of a lung cancer, a gastric cancer, a colon cancer, a liver cancer, a renal cell carcinoma, a bladder urothelial carcinoma, a metastatic melanoma, a breast cancer, an ovarian cancer, a cervical cancer, a head and neck cancer, a pancreatic cancer, an endometrial cancer, a prostate cancer, a thyroid cancer, a glioma, a glioblastoma, and other solid tumors, and a non- Hodgkin’ s lymphoma (NHL), Hodgkin’s lymphoma/disease (HD), an acute lymphocytic leukemia (ALL), a chronic lymphocytic leukemia (CLL), a chronic myelogenous leukemia (CML), a multiple myeloma (MM), an acute myeloid leukemia (AML), and other liquid tumors.
  • the cancer is a non- Hod
  • the composition comprises a therapeutically effective amount of an isolated polynucleotide, an isolated polypeptide, a host cell, and/or an iPSC or derivative cell thereof.
  • therapeutically effective amount refers to an amount of an active ingredient or component that elicits the desired biological or medicinal response in a subject.
  • a therapeutically effective amount can be determined empirically and in a routine manner, in relation to the stated purpose.
  • a therapeutically effective amount means an amount of the cells and/or the pharmaceutical composition that modulates an immune response in a subject in need thereof.
  • a therapeutically effective amount refers to the amount of therapy which is sufficient to achieve one, two, three, four, or more of the following effects: (i) reduce or ameliorate the severity of the disease, disorder or condition to be treated or a symptom associated therewith; (ii) reduce the duration of the disease, disorder or condition to be treated, or a symptom associated therewith; (iii) prevent the progression of the disease, disorder or condition to be treated, or a symptom associated therewith; (iv) cause regression of the disease, disorder or condition to be treated, or a symptom associated therewith; (v) prevent the development or onset of the disease, disorder or condition to be treated, or a symptom associated therewith; (vi) prevent the recurrence of the disease, disorder or condition to be treated, or a symptom associated therewith; (vii) reduce hospitalization of a subject having the disease, disorder or condition to be treated, or a symptom associated therewith; (viii) reduce hospitalization length of a subject having the disease, disorder or
  • the cells of the invention are allogeneic to the patient being treated.
  • the therapeutically effective amount or dosage can vary according to various factors, such as the disease, disorder or condition to be treated, the means of administration, the target site, the physiological state of the subject (including, e.g., age, body weight, health), whether the subject is a human or an animal, other medications administered, and whether the treatment is prophylactic or therapeutic. Treatment dosages are optimally titrated to optimize safety and efficacy.
  • compositions described herein are formulated to be suitable for the intended route of administration to a subject.
  • the compositions described herein can be formulated to be suitable for intravenous, subcutaneous, or intramuscular administration.
  • the cells of the application and/or the pharmaceutical compositions of the application can be administered in any convenient manner known to those skilled in the art.
  • the cells of the application can be administered to the subject by aerosol inhalation, injection, ingestion, transfusion, implantation, and/or transplantation.
  • the compositions comprising the cells of the application can be administered transarterially, subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, inrapleurally, by intravenous (i.v.) injection, or intraperitoneally.
  • the cells of the application can be administered with or without lymphodepletion of the subject.
  • compositions comprising cells of the application can be provided in sterile liquid preparations, typically isotonic aqueous solutions with cell suspensions, or optionally as emulsions, dispersions, or the like, which are typically buffered to a selected pH.
  • the compositions can comprise carriers, for example, water, saline, phosphate buffered saline, and the like, suitable for the integrity and viability of the cells, and for administration of a cell composition.
  • Sterile injectable solutions can be prepared by incorporating cells of the application in a suitable amount of the appropriate solvent with various other ingredients, as desired.
  • compositions can include a pharmaceutically acceptable carrier, diluent, or excipient such as sterile water, physiological saline, glucose, dextrose, or the like, that are suitable for use with a cell composition and for administration to a subject, such as a human.
  • a pharmaceutically acceptable carrier such as sterile water, physiological saline, glucose, dextrose, or the like
  • Suitable buffers for providing a cell composition are well known in the art.
  • Any vehicle, diluent, or additive used is compatible with preserving the integrity and viability of the cells of the application.
  • the cells of the application and/or the pharmaceutical compositions of the application can be administered in any physiologically acceptable vehicle.
  • a cell population comprising cells of the application can comprise a purified population of cells. Those skilled in the art can readily determine the cells in a cell population using various well known methods.
  • the ranges in purity in cell populations comprising genetically modified cells of the application can be from about 50% to about 55%, from about 55% to about 60%, from about 60% to about 65%, from about 65% to about 70%, from about 70% to about 75%, from about 75% to about 80%, from about 80% to about 85%, from about 85% to about 90%, from about 90% to about 95%, or from about 95% to about 100%. Dosages can be readily adjusted by those skilled in the art, for example, a decrease in purity could require an increase in dosage.
  • the cells of the application are generally administered as a dose based on cells per kilogram (cells/kg) of body weight of the subject to which the cells and/or pharmaceutical compositions comprising the cells are administered.
  • the cell doses are in the range of about 10 4 to about 10 10 cells/kg of body weight, for example, about 10 5 to about 10 9 , about 10 5 to about 10 8 , about 10 5 to about 10 7 , or about 10 5 to about 10 6 , depending on the mode and location of administration.
  • a higher dose is used than in regional administration, where the immune cells of the application are administered in the region of a tumor and/or cancer.
  • Exemplary dose ranges include, but are not limited to, 1 x 10 4 to 1 x 10 8 , 2 x 10 4 to 1 x 10 8 , 3 x 10 4 to 1 x 10 8 , 4 x 10 4 to 1 x 10 8 , 5 x 10 4 to 6 x 10 8 , 7 x 10 4 to 1 x 10 8 , 8 x 10 4 to 1 x 10 s , 9 x 10 4 to 1 x 10 8 , 1 x 10 5 to 1 x 10 8 , 1 x 10 5 to 9 x 10 7 , 1 x 10 5 to 8 x 10 7 , 1 x 10 5 to 7 x 10 7 , 1 x 10 5 to 6 x 10 7 , 1 x 10 5 to 5 x 10 7 , 1 x 10 3 to 4 x 10 7 , 1 x 10 5 to 4 x 10 7 ,
  • the dose can be adjusted to account for whether a single dose is being administered or whether multiple doses are being administered.
  • the precise determination of what would be considered an effective dose can be based on factors individual to each subject.
  • the terms “treat,” “treating,” and “treatment” are all intended to refer to an amelioration or reversal of at least one measurable physical parameter related to a cancer, which is not necessarily discernible in the subject, but can be discernible in the subject.
  • the terms “treat,” “treating,” and “treatment,” can also refer to causing regression, preventing the progression, or at least slowing down the progression of the disease, disorder, or condition.
  • “treat,” “treating,” and “treatment” refer to an alleviation, prevention of the development or onset, or reduction in the duration of one or more symptoms associated with the disease, disorder, or condition, such as a tumor or more preferably a cancer.
  • “treat,” “treating,” and “treatment” refer to prevention of the recurrence of the disease, disorder, or condition. In a particular embodiment, “treat,” “treating,” and “treatment” refer to an increase in the survival of a subject having the disease, disorder, or condition. In a particular embodiment, “treat,” “treating,” and “treatment” refer to elimination of the disease, disorder, or condition in the subject.
  • the cells of the application and/or the pharmaceutical compositions of the application can be administered in combination with one or more additional therapeutic agents.
  • the one or more therapeutic agents are selected from the group consisting of a peptide, a cytokine, a checkpoint inhibitor, a mitogen, a growth factor, a small RNA, a dsRNA (double stranded RNA), siRNA, oligonucleotide, mononuclear blood cells, a vector comprising one or more polynucleic acids of interest, an antibody, a chemotherapeutic agent or a radioactive moiety, or an immunomodulatory drug (IMiD).
  • IMD immunomodulatory drug
  • chemotherapeutic agents including alkylating agents such as thiotepa and cyclophaophamide, alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, corboquone; ethyleneimines and methylamelamines including altreamine, triethylenemelamine, trietyelenephosphoramide; delta-9-tetrahydocannabinol; a camptothecin, irinotecan , acetylcamptothecin, scopolectin, and 9-aminocamptothecin); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); podophyllotoxin; podophyllinic acid; teniposide; cryptophy
  • dynemicin including dynemicin A; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzmophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including ADRIAMYCIN®, morpholino-doxorubicin, cyanomorpholinodoxorubicin, 2-pyrrolino-doxorubicin, doxorubicin HC1 liposome injection (DOXIL®) and
  • anti HGF monoclonal antibodies e.g., AV299 from Aveo, AMG102, from Amgen
  • truncated mTOR variants e.g., CGEN241 from Compugen
  • protein kinase inhibitors that block mTOR induced pathways e.g.,ARQ197 from Arqule, XL880 from Exelexis, SGX523 from SGX Pharmaceuticals, MP470 from Supergen, PF2341066 from Pfizer
  • vaccines such as THERATOPE® vaccine and gene therapy vaccines, for example, ALLOVECTIN® vaccine, LEUVECTIN® vaccine, and VAXID® vaccine
  • topoisomerase 1 inhibitor e.g., LURTOTECAN®
  • rmRH e.g., ABARELIX®
  • lapatinib ditosylate an ErbB-2 and EGFR dual tyrosine kinase small
  • iPSCs Three methods can be used for creating the iPSCs that are used to make ab CAR-iT cells.
  • One route uses ab T cells that are collected from blood of donors. These T cells possess rearranged a and b gene clusters, so when they are reprogrammed to become iPSCs, the resulting TiPSCs (T cell-derived iPSCs) possess the same genetic rearrangements.
  • the ab TCRs have known antigen specificity and HLA-restriction (FIG. 1A).
  • Another method begins with a non-T cell from a donor.
  • the cell type can be any somatic cell, preferably cells used for this process are peripheral blood hematopoietic stem cells (HSCs) that are defined by expression of the surface protein CD34.
  • HSCs peripheral blood hematopoietic stem cells
  • PiPSC peripheral blood CD34 HSC-derived iPSCs
  • T-PiPSC TCR-expressing PiPSC
  • a third method uses ab T cells that are collected from blood of donors.
  • the ab T cells can be converted into a T-iPSC (TCR-expressing iPSC) via genetic engineering to replace the endogenous ab TCR locus with trusted rearranged ab TCR transgenes (FIG. 1C).
  • the rearranged TCR transgenes for a and b chains are delivered as a single polycistronic construct or as two separate constructs: one alpha and one beta.
  • PBMCs peripheral blood mononuclear cells
  • HSCs hematopoietic stem cells
  • the proliferating HSCs are subjected to iPSC reprogramming.
  • the iPSCs were reprogrammed using methods known in the art. Exemplary methods of iPSC reprogramming are described in U.S. Pat. Nos. 8,183,038; 8,268,620; 8,440,461; 9,499,786; 10,865,381; 8,952,801; 8,546,140; 9,644,184; 9,328,332; and 8,765,470, each of which is incorporated by reference in its entirety.
  • Any ab T cell can be reprogrammed into a TiPSC and the unknown TCR replaced with a known trusted TCR through genetic engineering (FIG. 1C).
  • FOG. 1C genetic engineering
  • PBMCs are collected from a donor and cultured in the presence of stimuli that cause mitosis of T cells. These can include antibodies that act as agonists for the CD3 molecule and CD28 molecule, non-specific mitogens such as phytohemmaglutinin (PHA), or other T cell mitogens.
  • PHA phytohemmaglutinin
  • iPSC reprogramming When employed in the presence of IL-2, mitogens cause T cell proliferation and render the T cells susceptible to iPSC reprogramming using methods known in the art. Exemplary methods of iPSC reprogramming are described in U.S. Pat. Nos. 8,183,038; 8,268,620; 8,440,461; 9,499,786; 10,865,381; 8,952,801; 8,546,140; 9,644,184; 9,328,332; and 8,765,470, each of which is incorporated by reference in its entirety.
  • the second approach to reprogramming TiPSC involves identification of specific T cells that carry specific TCR gene rearrangements which endow the encoded TCR with a known antigen and HLA specificity (FIG. 1 A). For example, T cells that recognize the influenza A antigenic peptide GILGFVFTL in the context of HLA-A*02:01 are collected, activated using mitogens and IL-2 and reprogrammed using methods known in the art. Exemplary methods of iPSC reprogramming are described in U.S. Pat. Nos. 8,183,038; 8,268,620; 8,440,461;
  • iPSC were cultured in HDM basal medium, composed of 50% Iscove’s Modified Dulbecco’s Medium and 50% Ham’s F12 Nutrient Mixture supplemented with B-27 Supplement, XenoFree, minus Vitamin A (IX), Non-Essential Amino Acids (IX), L-Ascorbic Acid Phosphate Magnesium Salt n-Hydrate (250 uM), Monothioglycerol (100 uM), and Heparin (100 ng/ml).
  • HDM basal medium composed of 50% Iscove’s Modified Dulbecco’s Medium and 50% Ham’s F12 Nutrient Mixture supplemented with B-27 Supplement, XenoFree, minus Vitamin A (IX), Non-Essential Amino Acids (IX), L-Ascorbic Acid Phosphate Magnesium Salt n-Hydrate (250 uM), Monothioglycerol (100 uM
  • HDM basal medium was supplemented with HI 152 (1 uM), CHIR99021 (2 uM), bFGF (50 ng/ml), and VEGF (50 ng/ml).
  • 80% of medium was removed and replaced with HDM basal medium supplemented with CHIR99021 (2 uM), bFGF (50 ng/ml), and VEGF (50 ng/ml).
  • 80% of medium was removed and replaced with HDM basal medium supplemented with BMP4 (25 ng/ml), bFGF (50 ng/ml), and VEGF (50 ng/ml).
  • HPCs were harvested between days 7-9 depending on starting iPSC source. HPC were defined as CD34+, CD43+, +/- CD45 on the cell surface.
  • the differentiation conditions for generation of alpha beta iPSC-derived T (ab iT) cells from ab T-HPCs are important, not only for optimal yield of iT cells having a TCR+ and CD3+ phenotype, but also for optimizing the function of the iT cell, including proliferation and target killing.
  • ab iT alpha beta iPSC-derived T
  • conditions were tested for improved yield, viability and phenotype, as well as fitness and target killing of the iT cell.
  • Illustrated herein is an exemplary method of differentiation of a CD34+ HPC to iT cell, wherein the CD34+ cell expresses a rearranged TCR, including but not limited to, a trusted rearranged TCR.
  • Notch signaling plays a key role in driving precursor cells towards a T cell fate.
  • the Notch family proteins DLL1, DLL4, and Jag2 (expressed by stromal cells in the thymus) signal through the receptor Notchl (expressed by early thymocytes).
  • DLL4 and DLL4 with JAG2 were cultured on plates coated using the following proteins for 21 to 35 days: recombinant Delta-like protein 4 (DLL4) with Retronectin® (Takara Bio, Shiga, Japan) and DLL4 with recombinant Jagged 2 (JAG2) and Retronectin®.
  • T cell differentiation medium used to differentiate HPCs to iT cells was composed of CTS AIM V Medium supplemented with CTS Immune Cell Serum Replacement (10%), Glutamax Supplement (IX), L- Ascorbic Acid Phosphate Magnesium Salt n-Hydrate (250 uM), and Nicotinamide (2 mM).
  • FIG. 2 demonstrates that the combination of DLL4 and JAG2 increased the yield of iT cells.
  • TCDM basal medium was supplemented with IL-2 and IL-7, with and without IL-15.
  • the addition of IL- 15 in the medium increased the yield of iT cells as well as the % viable iT cells at Day 28 (FIG. 3).
  • HPCs were generated from iPSCs engineered to express a CD 19-targeting CAR and cultured as described above.
  • those cultured on DLL4 and JAG2 coated plates had increased iT cell viability and an increase in lysis of CD19+ Reh target cells (FIG. 4).
  • UCHT1 When comparing OKT3 and UCHT1, UCHT1 supported more faithful T cell identity (TCR/CD3+) whereas 0KT3 elicited more CD56 expression (data not shown). When the antibodies were compared amongst cells treated with IL-15, UCHT1 resulted in higher iT yield as well as increased lysis of CD 19+ target cells (FIG. 5).
  • TCDM-I is TCDM basal medium supplemented with SCF (50 ng/ml), FLT3L (50 ng/ml), TPO (50 ng/ml), and IL-7 (50 ng/ml).
  • Cells were collected weekly and re-seeded on protein coated plates from days 1-14. At day 14 cells were cryopreserved. Cryopreserved cells were then thawed and seeded on DLL4/JAG2/RN coated plates in TCDM-I medium at 4.16E4 viable cells/cm2. Medium was changed every 24-72 hours using TCDM-I medium from days 14-21. At day 21, cells were collected and seeded at 8.3E4 viable cells/cm2 on UCHT1 anti-CD3 Ab (2 ug/ml) admixed with MOPC-21 mouse IgG Isotype Ab (Melchers, Biochem J. 1970 Oct;l 19(4):765-72) (8 ug/ml) coated plates in TCDM + IL-2, IL-7, IL-15. At day 28 cells were collected for evaluation (FIG 6).
  • a T-iPSC line that was derived from an ab T cell expressing a TCR having unknown- specificity were engineered to express a CD 19-targeting CAR to evaluate their tumor cell killing activity.
  • the CAR-T-iPSC cells were used to differentiate ab T cells using the method described in Example 1. After 28 days of differentiation, cells were collected and stained for lineage markers, maturation markers and cytokine receptors, and then analyzed by flow cytometry (FIG. 7). The majority of cells were CD45-positive. CD45-expressing cells were analyzed for all other markers. The CD45-positive cells co-expressed TCRo$ and CD3. Most of the CD3-positive cells are CD56-negative. The majority of cells expressed CD7 with a subset positive for both CD7 and CD5. When CD8 was expressed, it was as a heterodimer of CD8a and E ⁇ 8b. No CD4 expression was detected. Expression of co-stimulatory molecules CD28 and CD27 was low.
  • CAR-iT cells expressed IL-2 family cytokine receptors including CD25, CD122, CD127, CD132 and CD215. Further, Day 28 CAR-iT cells were left unstained or stained with anti-FMC63 CAR antibody. Most (74%) of the CAR-iT cells expressed the CAR protein on their surface (FIG. 8). The CAR-iT cells were then assessed for antigen-specific killing of B cell lymphoma cells (Reh). For these studies, either Reh cells or a version of Reh cells where the CD19 gene was knocked out to make CD19-negative cells were used. Either CAR-iT cells or PBMC-derived CART cells were co-cultured at a 1:1 ratio with target cells. Target cell killing was measured using an IncuCyte instrument.
  • Public TCRs are those sequences that occur frequently in multiple individuals with a certain HLA type. For example, there are public TCRs that recognize an antigenic peptide sequence of the influenza A virus matrix protein (epitope: GILGFVFTL) in the context of the HLA-I molecule HLA-A*02:01. Most, if not all, people who carry the HLA-A*02:01 allele and who have been exposed to influenza A will also have T cells that share a common public TCR. The homology of such public TCRs can be described at two levels.
  • TCR alpha V TCR alpha V
  • TRBV TCR beta V
  • TRBJ joining
  • public TCR allotypes The physical intersection of rearranged V gene, D gene and J gene (beta chain) or V gene and J gene (alpha chain) along with n/p additions, comprises the part of the TCR that confers specificity for an antigen - the so-called complementarity determining region 3 (CDR3).
  • CDR3 complementarity determining region 3
  • Example of public TCR types bases on differing levels of identity Those individuals who carry HLA-A*02:01 will also carry a second HLA-A gene (usually not HLA-A*02:01), two HLA-B genes, and two HLA-C genes, and because those other genes are diverse between individuals, the public TCR allotypes and sequences have been de- risked in nature (FIG. 11). That is, these TCRs are exposed to a vast diversity of other non-HLA- A*02 proteins during thymic selection and they are not purged. Thus, these TCRs fail to recognize non-HLA-A*02 molecules and are unlikely to participate in graft versus host disease, even in people who lack HLA-A*02:01.
  • PiPSCs were engineered to express a recombinant public rearranged ab TCR having an alpha chain of SEQ ID NO: 84 and a beta chain of SEQ ID NO: 85 according to the method shown in FIG. IB.
  • the recombinant public rearranged ab TCR recognizes the influenza epitope GILGFVFTL (SEQ ID NO: 83) in the context of HLA-A* 02:01.
  • the transgene was under control of a constitutive CAG promoter.
  • Nalm6 cells, a B cell precursor leukemia cell line, engineered to express a negative control or GILGFVFTL epitope were cultured with the engineered ab iT cells at a 1 : 1 or 5: 1 effector to target ratio.
  • FIG. 12 shows that ab iT cells engineered to express the public TCR were able to kill target cells expressing the flu epitope, demonstrating that the genomic engineered public TCR was functional.

Abstract

Provided are method for generating αβ T cells from induced pluripotent stem cells. Also provided are genetically engineered iPSCs, αβ T cells, CAR-αβ T cells, and methods of using the same.

Description

COMPOSITIONS AND METHODS FOR GENERATING ALPHA-BETA T CELLS FROM INDUCED PLURIPOTENT STEM CELLS
CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Patent Application No. 63/171,650 filed April 7, 2021, which is incorporated by reference herein in its entirety.
TECHNICAL FIELD
This application provides genetically engineered induced pluripotent stem cells (iPSCs) and derivative cells thereof expressing a rearranged ab T cell receptor (TCR). Also provided are uses of the iPSCs or derivative cells thereof to express a chimeric antigen receptor for allogenic cell therapy. Further provided are related vectors, polynucleotides, and pharmaceutical compositions.
REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY This application contains a sequence listing, which is submitted electronically via EFS- Web as an ASCII formatted sequence listing with a file name “Sequence Listing_ST25” and a creation date of March 29, 2022, and having a size of 158 kb. The sequence listing submitted via EFS-Web is part of the specification and is herein incorporated by reference in its entirety.
BACKGROUND
Chimeric antigen receptor (CAR) T (CART) cells have revolutionized cancer therapies by providing a new approach to eliminate malignant cells in an antigen-specific manner. Currently approved versions of CART are autologous products wherein the CAR molecule is delivered as a transgene using a lentiviral vector. While efficacious, significant limitations of this method include the duration of manufacturing, the cost of manufacturing, poor T cell health in many cancer patients which renders the cell product inferior, and inability to generate multiple doses for repeat treatments. Some of these limitations are being addressed by development of allogenic methods wherein peripheral blood T cells from a healthy donor are used to manufacture multiple doses of CART as an off-the-shelf product. However, new challenges emerge for this platform. First, one healthy donor can only support a limited number of new doses from a leukapheresis product, leading to significant lot to lot variability depending on the donor. This approach requires numerous parallel manufacturing campaigns which is inefficient and needlessly expensive. Second, variability of human leukocyte antigens (HLA) renders such allogenic products susceptible to immune rejection by the recipient. Third, T cell receptors (TCRs) expressed by the donor T cells are incompatible for the mismatched HLA molecules of the recipient and can thus participate in graft versus host disease, a potentially life-threatening complication of T cell allografts.
Thus, there is a need in the art for allogenic CART therapies that can be manufactured in a large batch, while also mitigating the risk of graft versus host disease.
A trusted TCR is a specific T cell receptor with a reduced likelihood of causing graft versus host disease. TCRs are diverse heterodimeric cell surface receptors that arise during the process of thymic selection during T cell development. The random nature of TCR rearrangement results in mature TCR protein complexes that are capable of recognizing antigens in the context of HLA-mediated antigen presentation. To prevent such TCRs from recognizing self-antigens in the context of self-HLA, a specific stage of T cell development is dedicated to removal of such ‘ autoreactive ’ T cells. This process is called negative selection. In the thymus, when an autoreactive pre-T cell (thymocyte) recognizes self-antigen in the context of self-HLA via its TCR, that pre-T cell is eliminated through a programmed cell death response. Thus, the diverse T cell pool is purged of any potentially harmful autoreactive T cells. However, because this process is highly specific to the individual, negative selection does not eliminate T cells that might react to antigens/HLA in another individual. This is the fundamental basis for graft versus host disease wherein allogenic T cell grafts include some cells that can recognize the antigen/HLA complexes of the recipient and then attack the recipient cells.
Several studies have described the diversity of TCR sequences in populations of people. While the vast majority of TCR sequences are so-called ‘private’ sequences (occurring only infrequently in different people), a portion of TCRs found in humans are public (occurring frequently amongst people with a shared HLA or shared infectious agent) (DeWitt et al., Elife. 2018 Aug 28;7:e38358.). Within known public TCRs, there are well-characterized receptors that recognize specific viruses in people with specific HLA-alleles. One of these is a TCR using the TRBV19 gene which recognizes an influenza A epitope in the context of HLA-A*02:01 (DeWitt et al., Elife. 2018 Aug 28;7:e38358). Such TRBV19 TCRs often pair with an alpha TCR chain TRAV27 and recognize the influenza peptide GILGFVFTL (Choo et al., J Virol. 2014 Sep;88(l 8): 10613-23; Chen et al., Cell Rep. 2017 Apr 18;19(3):569-583).
Described herein are methods for generating CAR T cells expressing a trusted TCR derived from induced pluripotent stem cells (iPSCs).
BRIEF SUMMARY
In one general aspect, provided is a genetically engineered induced pluripotent stem cell or a derivative cell thereof. The cell comprises (i) one or more polynucleotides encoding a recombinant rearranged ab T cell receptor (TCR); and (ii) a polynucleotide encoding a chimeric antigen receptor (CAR), wherein the rearranged ab TCR is a public TCR that specifically recognizes a non-human antigen in the context of a specific HLA class I (HLA-I) allele and wherein the rearranged ab TCR supports differentiation of the iPSC to a T cell.
In certain embodiments, the rearranged ab TCR enables expansion of the T cell differentiated from the iPSC after mitogenic stimulation.
In certain embodiments, the one or more polynucleotides encoding the recombinant rearranged ab TCR comprise an a TCR variable gene selected from the group consisting of TRAV27 and TRAV13-1; an a TCRjoining gene selected from the group consisting of TRAJ41 and TRAJ37; and an a TCR constant gene TRAC.
In certain embodiments, the one or more polynucleotides encoding the recombinant rearranged ab TCR comprise a b chain variable gene TRBV19; a b chain variable gene selected from the group consisting of TRBJ2-7, TRBJ2-5, and TRBJ2-6; a b chain constant gene selected from the group consisting of TRBC1 and TRBC2.
In certain embodiments, the recombinant rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza- A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
In certain embodiments, the iPSC is reprogrammed from peripheral blood mononuclear cells (PBMCs), preferably CD34+ hematopoietic stem cells (HSCs) or ab T cells.
Also provided is a T cell derived from the iPSC cell according to the application.
Also provided is an induced pluripotent stem cell (iPSC) or a T cell derived therefrom comprising: one or more polynucleotides encoding a rearranged ab T cell receptor (TCR), wherein the rearranged ab TCR is a public TCR that specifically recognizes a non-human antigen in the context of a specific HLA class I (HLA-I) allele and the rearranged ab TCR supports differentiation of the iPSC to the T cell, and an exogenous polynucleotide encoding a chimeric antigen receptor (CAR); and one or more of the following additional features:
(a) an exogenous polynucleotide encoding an artificial cell death polypeptide;
(b) a deletion or reduced expression of one or more of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CUT A, RFX5 and RFXAP genes;
(c) a deletion or reduced expression of RAG1 and RAG2 genes;
(d) an exogenous polynucleotide encoding a non-naturally occurring variant of FcyRIII (CD 16);
(e) an exogenous polynucleotide encoding interleukin 15 (IL-15) and/or IL-15 receptor or a variant or truncation thereof;
(f) an exogeneous polynucleotide encoding a constitutively active interleukin 7 (IL- 7) receptor or variant thereof;
(g) an exogenous polynucleotide encoding interleukin 12 (IL-12) or interleukin 21 (IL- 21) or a variant thereof;
(h) an exogenous polynucleotide encoding human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G);
(i) an exogenous polynucleotide encoding leukocyte surface antigen cluster of differentiation CD47 (CD47) and/or CD24; or an exogenous polynucleotide encoding one or more imaging or reporter proteins, such as PSMA or HSV-tk.
In certain embodiments, the rearranged ab TCR is recombinant.
In certain embodiments, the iPSC is reprogrammed from peripheral blood mononuclear cells (PBMCs), preferably CD34+ hematopoietic stem cells (HSCs) or ab T cells.
In certain embodiments, the rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
In certain embodiments, the iPSC or T cell comprises an exogenous polynucleotide encoding a human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G).
In certain embodiments, one or more of the exogenous polynucleotides are integrated at one or more loci on the chromosome of the cell selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, HI 1, GAPDH, RUNX1, B2M, TAPI, TAP2, Tapasin,
NLRC5, CIITA, RFXANK, CIITA, RFX5, RFXAP, TRAC, TRBCl, TRBC2, RAG1, RAG2, NKG2A, NKG2D, CD38, CIS, CBL-B, SOCS2, PD1, CTLA4, LAG3, TIM3, or TIGIT genes, provided at least one of the exogenous polynucleotides is integrated at a locus of a gene selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes to thereby result in a deletion or reduced expression of the gene.
In certain embodiments, one or more of the exogenous polynucleotides are integrated at the loci of the CIITA, AAVS1 and B2M genes.
In certain embodiments, the iPSC or T cell has a deletion or reduced expression of one or more of B2M or CIITA genes.
In certain embodiments, the rearranged ab TCR comprises an a TCR chain having a CDR3 of the amino acid sequence of SEQ ID NO: 84, and a b TCR chain having a CDR3 of the amino acid sequence of SEQ ID NO: 85.
In certain embodiments, the ab TCR comprises an a TCR chain comprising the amino acid sequence encoded by TRAV27 and TRAJ41 genes, and having the CDR3 of the amino acid sequence of SEQ ID NO: 84, and the b TCR chain comprising the amino acid sequence encoded by TRBV19 and TRBJ2-7 genes, and having the CDR3 of the amino acid sequence of SEQ ID NO: 85.
In certain embodiments, the CAR comprises:
(i) a signal peptide comprising a signal peptide;
(ii) an extracellular domain comprising a binding domain that specifically binds an antigen on a target cell;
(iii) a hinge region;
(iv) a transmembrane domain;
(v) an intracellular signaling domain; and
(vi) a co-stimulatory domain.
In certain embodiments, the signal peptide is GMCSF signal peptide.
In certain embodiments, the extracellular domain comprises an scFv or VHH derived from an antibody that specifically binds an antigen that is expressed on cancer cells.
In certain embodiments, the hinge region comprises a CD28 hinge region, a CD8 hinge region, or an IgG hinge region. In certain embodiments, the transmembrane domain comprises a CD28 transmembrane domain or a CD8 transmembrane domain.
In certain embodiments, the intracellular signaling domain is derived from DAP10,
DAP 12, Fc epsilon receptor I g chain (FCER1G), FcR b, NKG2D, CD35, CD3c, CD3y, Oϋ3z, CD5, CD22, CD226, CD66d, CD79A, or CD79B.
In certain embodiments, the co-stimulatory domain is a co-stimulatory signaling domains are derived from CD28, 41BB, IL2Rb, CD40, 0X40 (CD134), CD80, CD86, CD27, ICOS, NKG2D, DAP 10, DAP 12, or 2B4 (CD244).
In certain embodiments, the CAR comprises:
(i) the signal peptide comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 1;
(ii) the extracellular domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 7;
(iii) the hinge region comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 22;
(iv) the transmembrane domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 24;
(v) the intracellular signaling domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 6; and
(vi) the co-stimulatory domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 20.
In certain embodiments, the mechanism of action of the artificial cell death polypeptide is metabolic, dimerization-inducing or therapeutic monoclonal antibody-mediated.
In certain embodiments, the therapeutic monoclonal antibody mediated artificial cell death polypeptide is an inactivated cell surface protein selected from the group of monoclonal antibody specific epitopes selected from epitopes specifically recognized by ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, polatuzumab vedotin, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimumab, belimumab, canakinumab, denosumab, golimumab, ipilimumab, ofatumumab, panitumumab, or ustekinumab.
In certain embodiments, the inactivated cell surface protein is a truncated epithelial growth factor (tEGFR) variant.
In certain embodiments, the tEGFR variant consists of an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 71.
In certain embodiments, the HLA-E comprises an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 66 or the HLA-G comprises an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 69.
In certain embodiments, (i) the exogenous polynucleotide encoding the chimeric antigen receptor (CAR) is integrated at a locus of AAVS1 gene; (ii) the exogenous polypeptide encoding the artificial cell death polypeptide is integrated at a locus of CIITA gene; and (iii) the exogenous polypeptide encoding the human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G) is integrated at a locus of B2M gene; wherein integration of the exogenous polynucleotides deletes or reduces expression of CIITA and B2M.
Also provided is an induced pluripotent stem cell (iPSC) or a T cell comprising:
(i) an exogenous polynucleotide encoding a chimeric antigen receptor (CAR) having the amino acid sequence of SEQ ID NO: 61;
(ii) an exogenous polynucleotide encoding an artificial cell death polypeptide comprising an apoptosis-inducing domain having the amino acid sequence of SEQ ID NO: 71;
(iii) a polynucleotide encoding a rearranged T cell receptor (TCR) locus comprising a a TCR having the amino acid sequence of SEQ ID NO: 86, and a b TCR having the amino acid sequence of SEQ ID NO: 87; and (iv) optionally, an exogenous polynucleotide encoding a human leukocyte antigen E (HLA-E) having the amino acid sequence of SEQ ID NO: 66; wherein one or more of the exogenous polynucleotides are integrated at loci of AAVS1, CIITA and B2M genes, to thereby delete or reduce expression of CIITA and B2M.
Also provided is a composition comprising the T cell according embodiments of the application.
In certain embodiments, the composition further comprises or is provided or used in combination with, one or more therapeutic agents selected from the group consisting of a peptide, a cytokine, a checkpoint inhibitor, a mitogen, a growth factor, a small RNA, a dsRNA (double stranded RNA), siRNA, oligonucleotide, mononuclear blood cells, a vector comprising one or more polynucleic acids of interest, an antibody, a chemotherapeutic agent or a radioactive moiety, or an immunomodulatory drug (IMiD).
Also provided is a method of treating cancer in a subject in need thereof, comprising administering the cell according to embodiments of the application or the composition according to embodiments of the application to the subject in need thereof.
Also provided is a method of manufacturing a T cell of the application comprising differentiating an iPSC cell of the application under conditions for cell differentiation to thereby obtain the T cell. In certain embodiments, the iPSC is obtained by genomic engineering an iPSC, wherein the genomic engineering comprises targeted editing. Examples of targeted editing include, but are not limited to, deletion, insertion, or in/del carried out by CRISPR, ZFN, TALEN, homing nuclease, homology recombination, or any other functional variation of these methods.
Also provided is a CD34+ hematopoietic progenitor cell (HPC) derived from an induced pluripotent stem cell (iPSC) comprising one or more polynucleotides encoding a rearranged ab T cell receptor (TCR), wherein the rearranged ab TCR is a public TCR that specifically recognizes a non-human antigen in the context of a specific HLA class I (HLA-I) allele and the rearranged ab TCR supports differentiation of the iPSC to a T cell, and an exogenous polynucleotide encoding a chimeric antigen receptor (CAR); and one or more of the following additional features:
(a) an exogenous polynucleotide encoding an artificial cell death polypeptide; (b) a deletion or reduced expression of one or more of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CUT A, RFX5 and RFXAP genes;
(c) a deletion or reduced expression of RAG1 and RAG2 genes;
(d) an exogenous polynucleotide encoding a non-naturally occurring variant of FcyRIII (CD 16);
(e) an exogenous polynucleotide encoding interleukin 15 (IL-15) and/or interleukin (IL-15) receptor or a variant or truncation thereof;
(f) an exogeneous polynucleotide encoding a constitutively active interleukin 7 (IL- 7) receptor or variant thereof;
(g) an exogenous polynucleotide encoding interleukin 12 (IL-12) or interleukin 21 (IL-21) or a variant thereof;
(h) an exogenous polynucleotide encoding human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G);
(i) an exogenous polynucleotide encoding leukocyte surface antigen cluster of differentiation CD47 (CD47) and/or CD24; or an exogenous polynucleotide encoding one or more imaging or reporter proteins, such as PSMA or HSV-tk.
Also provided is a method of differentiating CD34+ hematopoietic progenitor cell (HPC) comprising a polynucleotide encoding a rearranged TCR, such as an induced-pluripotent stem cell (iPSC)-derived CD34+ HPC comprising a polynucleotide encoding a rearranged TCR, to a T cell, the method comprising culturing the CD34+ HPC in a medium comprising Delta-like protein 4 (DLL4) and Jagged 2 (JAG2), optionally further comprising a fibronectin protein or fragment thereof, SCF, FLT3L, TPO, and/or IL-7.
Also provided is a method of differentiating an induced-pluripotent stem cell (iPSC)- derived CD34+ hematopoietic progenitor cell (HPC) comprising a polynucleotide encoding a rearranged TCR, the method comprising:
(a) culturing the cell in medium comprising recombinant Delta-like protein 4 (DLL4) and recombinant Jagged 2 (JAG2), optionally further comprising a fibronectin protein or fragment thereof;
(b) culturing the cell in medium comprising interleukin-2 (IL-2), IL-7, and IL-15; and (c) culturing the cell in medium comprising an anti-CD3 antibody, preferably OKT3 or UCHT1.
In certain embodiments, the DLL4 and JAG2 proteins are immobilized on a cell culture plate, such as by using poly dopamine in the presence or absence of Protein G coating.
Also provided is a recombinant Delta-like protein 4 (DLL4) variant polypeptide having an amino acid comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 90.
Also provided is a method of differentiating an induced-pluripotent stem cell (iPSC)- derived CD34+ hematopoietic progenitor cell (HPC) comprising a polynucleotide encoding a rearranged TCR to a T cell, the method comprising culturing the CD34+ HPC in a medium comprising a recombinant DLL4 variant according to embodiments of the application.
BRIEF DESCRIPTION OF THE DRAWINGS
The foregoing summary, as well as the following detailed description of preferred embodiments of the present application, will be better understood when read in conjunction with the appended drawings. It should be understood, however, that the
FIGS. 1A-C show schematics of methods of generating ab iT cells using induced pluripotent stem cells (iPSCs) as a source. FIG. 1A shows a method of generating ab T cells using iPSCs derived from mature ab T cells with a known antigen specificity and HLA- restriction collected from a blood sample. FIG. IB shows a method of generating ab iT cells using iPSCs derived from CD34+ hematopoietic stem cells (HSC) collected from a blood sample. FIG. 1C shows a method of generating ab iT cells using iPSCs derived from mature ab T cells collected from a blood sample with TCR of unknown antigen specificity replaced by trusted TCR.
FIG. 2 shows iPSC-derived T (iT) yield when hematopoietic progenitor cells (HPCs) are differentiated in DLL4 or DLL4 and JAG2.
FIG. 3 shows iPSC-derived T (iT) cell yield and percent viability of iT cells differentiated from hematopoietic progenitor cells (HPCs) culture with and without interleukin- 15 (IL-15). FIG. 4 shows the percent viability of iPSC-derived T (iT) engineered to express a CD 19 and percent lysis of target cells by iPSC-derived T (iT) engineered to express a CD 19 targeting chimeric antigen receptor (CAR) in iT cells differentiated in DLL4 or DLL4 and JAG2.
FIG. 5 shows iPSC-derived T (iT) cell yield and percent lysis of target cells by iPSC- derived T (iT) engineered to express a CD19 in iT cells differentiated in the anti-CD3 antibodies OKT3 or UCHTl.
FIG. 6 is a schematic of a method for differentiating hematopoietic progenitor cells (HPCS) to iPSC-derived T (iT) cells.
FIG. 7 shows graphs of representative FACS results showing cell markers expressed by iPSC-derived ab T (iT) cells after 28 days of differentiation.
FIG. 8 shows expression of FMC63 (CD19-specific) CAR on iT cells. CAR-iT cells were left unstained (top) or stained with anti-FMC63 CAR antibody (bottom).
FIGs. 9A-B shows antigen-specific killing of B cell lymphoma cells by CAR-iT cells. FIG. 9 A shows antigen-positive Reh lymphoma cells (CD 19-expressing lymphoma line) killing by either CAR-iT cells (black squares) or PBMC -derived CART cells (grey circles). FIG. 9B shows antigen-negative Reh lymphoma cells (CD 19 antigen removed by genetic deletion) by either CAR-iT cells (black squares) or PBMC-derived CART cells (grey circles).
FIG. 10 shows a schematic of the alpha TCR chain and beta TCR chain of a public TCR.
FIG. 11 shows exemplary HLA-restricted TCR combinations.
FIG. 12 shows the percent viability of NALM6 cells expressing a negative control or an influenza peptide (GILGFVFTL) cultured with ab iT cells engineered to express a trusted TCR which targets the influenza peptide at an effector to target ratio of 1 : 1 or 5: 1.
DETAILED DESCRIPTION
Various publications, articles and patents are cited or described in the background and throughout the specification; each of these references is herein incorporated by reference in its entirety. Discussion of documents, acts, materials, devices, articles or the like which has been included in the present specification is for the purpose of providing context for the invention. Such discussion is not an admission that any or all of these matters form part of the prior art with respect to any inventions disclosed or claimed. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this application pertains. Otherwise, certain terms used herein have the meanings as set forth in the specification.
It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise.
Unless otherwise stated, any numerical values, such as a concentration or a concentration range described herein, are to be understood as being modified in all instances by the term “about.” Thus, a numerical value typically includes ± 10% of the recited value. For example, a concentration of 1 mg/mL includes 0.9 mg/mL to 1.1 mg/mL. Likewise, a concentration range of 1% to 10% (w/v) includes 0.9% (w/v) to 11% (w/v). As used herein, the use of a numerical range expressly includes all possible subranges, all individual numerical values within that range, including integers within such ranges and fractions of the values unless the context clearly indicates otherwise.
Unless otherwise indicated, the term “at least” preceding a series of elements is to be understood to refer to every element in the series. Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the application described herein. Such equivalents are intended to be encompassed by the application.
As used herein, the terms “comprises,” “comprising,” “includes,” “including,” “has,” “having,” “contains” or “containing,” or any other variation thereof, will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers and are intended to be non-exclusive or open-ended. For example, a composition, a mixture, a process, a method, an article, or an apparatus that comprises a list of elements is not necessarily limited to only those elements but can include other elements not expressly listed or inherent to such composition, mixture, process, method, article, or apparatus. Further, unless expressly stated to the contrary, “or” refers to an inclusive or and not to an exclusive or. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).
As used herein, the conjunctive term “and/or” between multiple recited elements is understood as encompassing both individual and combined options. For instance, where two elements are conjoined by “and/or,” a first option refers to the applicability of the first element without the second. A second option refers to the applicability of the second element without the first. A third option refers to the applicability of the first and second elements together. Any one of these options is understood to fall within the meaning, and therefore satisfy the requirement of the term “and/or” as used herein. Concurrent applicability of more than one of the options is also understood to fall within the meaning, and therefore satisfy the requirement of the term “and/or.”
As used herein, the term “consists of,” or variations such as “consist of’ or “consisting of,” as used throughout the specification and claims, indicate the inclusion of any recited integer or group of integers, but that no additional integer or group of integers can be added to the specified method, structure, or composition.
As used herein, the term “consists essentially of,” or variations such as “consist essentially of’ or “consisting essentially of,” as used throughout the specification and claims, indicate the inclusion of any recited integer or group of integers, and the optional inclusion of any recited integer or group of integers that do not materially change the basic or novel properties of the specified method, structure or composition. See M.P.E.P. § 2111.03.
As used herein, “subject” means any animal, preferably a mammal, most preferably a human. The term “mammal” as used herein, encompasses any mammal. Examples of mammals include, but are not limited to, cows, horses, sheep, pigs, cats, dogs, mice, rats, rabbits, guinea pigs, monkeys, humans, etc., more preferably a human.
It should also be understood that the terms “about,” “approximately,” “generally,” “substantially,” and like terms, used herein when referring to a dimension or characteristic of a component of the preferred invention, indicate that the described dimension/characteristic is not a strict boundary or parameter and does not exclude minor variations therefrom that are functionally the same or similar, as would be understood by one having ordinary skill in the art. At a minimum, such references that include a numerical parameter would include variations that, using mathematical and industrial principles accepted in the art (e.g., rounding, measurement or other systematic errors, manufacturing tolerances, etc.), would not vary the least significant digit.
The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences (e.g., CAR polypeptides and the CAR polynucleotides that encode them), refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat’l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by visual inspection {see generally, Current Protocols in Molecular Biology, F.M. Ausubel et al, eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1995 Supplement) (Ausubel)).
Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1990) . Mol. Biol. 215: 403-410 and Altschul et al. (1997) Nucleic Acids Res. 25: 3389- 3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul etal, supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased.
Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always > 0) and N (penalty score for mismatching residues; always < 0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N= -4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).
In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul,
Proc. Nat’l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
A further indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the polypeptide encoded by the second nucleic acid, as described below. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules hybridize to each other under stringent conditions.
As used herein, the term “isolated” means a biological component (such as a nucleic acid, peptide, protein, or cell) has been substantially separated, produced apart from, or purified away from other biological components of the organism in which the component naturally occurs, i.e., other chromosomal and extrachromosomal DNA and RNA, proteins, cells, and tissues. Nucleic acids, peptides, proteins, and cells that have been “isolated” thus include nucleic acids, peptides, proteins, and cells purified by standard purification methods and purification methods described herein. “Isolated” nucleic acids, peptides, proteins, and cells can be part of a composition and still be isolated if the composition is not part of the native environment of the nucleic acid, peptide, protein, or cell. The term also embraces nucleic acids, peptides and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.
The term "recombinant" refers to a biomolecule that (1) has been removed from its naturally occurring environment, (2) is not associated with all or a portion of another biomolecule in which the biomolecule is found in nature, (3) is operatively linked to another biomolecule which it is not linked to in nature, or (4) does not occur in nature. Examples of biomolecule include, e.g., a nucleic acid or a polypeptide. The term "recombinant" can be used in reference to cloned DNA isolates, chemically synthesized polynucleotide or polypeptide, or analogs thereof, or polynucleotide or polypeptide, or analogs thereof that are biologically synthesized by heterologous systems, as well as proteins and/or mRNAs encoded by such recombinant nucleic acids.
As used herein, the term “polynucleotide,” synonymously referred to as “nucleic acid molecule,” “nucleotides” or “nucleic acids,” refers to any polyribonucleotide or polydeoxyribonucleotide, which can be unmodified RNA or DNA or modified RNA or DNA. “Polynucleotides” include, without limitation single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that can be single-stranded or, more typically, double-stranded or a mixture of single- and double- stranded regions. In addition, “polynucleotide” refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The term polynucleotide also includes DNAs or RNAs containing one or more modified bases and DNAs or RNAs with backbones modified for stability or for other reasons. “Modified” bases include, for example, tritylated bases and unusual bases such as inosine. A variety of modifications can be made to DNA and RNA; thus, “polynucleotide” embraces chemically, enzymatically or metabolically modified forms of polynucleotides as typically found in nature, as well as the chemical forms of DNA and RNA characteristic of viruses and cells. “Polynucleotide” also embraces relatively short nucleic acid chains, often referred to as oligonucleotides.
A “construct” refers to a macromolecule or complex of molecules comprising a polynucleotide to be delivered to a host cell, either in vitro or in vivo. A “vector,” as used herein refers to any nucleic acid construct capable of directing the delivery or transfer of a foreign genetic material to target cells, where it can be replicated and/or expressed. The term “vector” as used herein comprises the construct to be delivered. A vector can be a linear or a circular molecule. A vector can be integrating or non-integrating. The major types of vectors include, but are not limited to, plasmids, episomal vector, viral vectors, cosmids, and artificial chromosomes. Viral vectors include, but are not limited to, adenovirus vector, adeno-associated virus vector, retrovirus vector, lentivirus vector, Sendai virus vector, and the like.
By “integration” it is meant that one or more nucleotides of a construct is stably inserted into the cellular genome, i.e., covalently linked to the nucleic acid sequence within the cell's chromosomal DNA. By “targeted integration” it is meant that the nucleotide(s) of a construct is inserted into the cell's chromosomal or mitochondrial DNA at a pre-selected site or “integration site”. The term “integration” as used herein further refers to a process involving insertion of one or more exogenous sequences or nucleotides of the construct, with or without deletion of an endogenous sequence or nucleotide at the integration site. In the case, where there is a deletion at the insertion site, “integration” can further comprise replacement of the endogenous sequence or a nucleotide that is deleted with the one or more inserted nucleotides.
As used herein, the term “exogenous” is intended to mean that the referenced molecule or the referenced activity is introduced into, or non-native to, the host cell. The molecule can be introduced, for example, by introduction of an encoding nucleic acid into the host genetic material such as by integration into a host chromosome or as non- chromosomal genetic material such as a plasmid. Therefore, the term as it is used in reference to expression of an encoding nucleic acid refers to introduction of the encoding nucleic acid in an expressible form into the cell. The term “endogenous” refers to a referenced molecule or activity that is present in the host cell in its native form. Similarly, the term when used in reference to expression of an encoding nucleic acid refers to expression of an encoding nucleic acid natively contained within the cell and not exogenously introduced.
As used herein, a “gene of interest” or “a polynucleotide sequence of interest” is a DNA sequence that is transcribed into RNA and in some instances translated into a polypeptide in vivo when placed under the control of appropriate regulatory sequences. A gene or polynucleotide of interest can include, but is not limited to, prokaryotic sequences, cDNA from eukaryotic mRNA, genomic DNA sequences from eukaryotic (e.g., mammalian) DNA, and synthetic DNA sequences. For example, a gene of interest may encode an miRNA, an shRNA, a native polypeptide (i.e. a polypeptide found in nature) or fragment thereof; a variant polypeptide (i.e. a mutant of the native polypeptide having less than 100% sequence identity with the native polypeptide) or fragment thereof; an engineered polypeptide or peptide fragment, a therapeutic peptide or polypeptide, an imaging marker, a selectable marker, and the like.
“Operably-linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably-linked with a coding sequence or functional RNA when it is capable of affecting the expression of that coding sequence or functional RNA (i.e., the coding sequence or functional RNA is under the transcriptional control of the promoter). Coding sequences can be operably- linked to regulatory sequences in sense or antisense orientation.
The term “expression” as used herein, refers to the biosynthesis of a gene product. The term encompasses the transcription of a gene into RNA. The term also encompasses translation of RNA into one or more polypeptides, and further encompasses all naturally occurring post- transcriptional and post-translational modifications. The expressed CAR can be within the cytoplasm of a host cell, into the extracellular milieu such as the growth medium of a cell culture or anchored to the cell membrane.
As used herein, the terms “peptide,” “polypeptide,” or “protein” can refer to a molecule comprised of amino acids and can be recognized as a protein by those of skill in the art. The conventional one-letter or three-letter code for amino acid residues is used herein. The terms “peptide,” “polypeptide,” and “protein” can be used interchangeably herein to refer to polymers of amino acids of any length. The polymer can be linear or branched, it can comprise modified amino acids, and it can be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component. Also included within the definition are, for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids, etc.), as well as other modifications known in the art.
The peptide sequences described herein are written according to the usual convention whereby the N-terminal region of the peptide is on the left and the C-terminal region is on the right. Although isomeric forms of the amino acids are known, it is the L-form of the amino acid that is represented unless otherwise expressly indicated.
As used herein, the term “engineered immune cell” refers to an immune cell, also referred to as an immune effector cell, that has been genetically modified by the addition of exogenous genetic material in the form of DNA or RNA to the total genetic material of the cell.
Induced Pluripotent Stem Cells (iPSCs) And Immune Effector Cells
IPSCs have unlimited self-renewing capacity. Use of iPSCs enables cellular engineering to produce a controlled cell bank of modified cells that can be expanded and differentiated into desired immune effector cells, supplying large amounts of homogeneous allogeneic therapeutic products.
Provided herein are genetically engineered iPSCs and derivative cells thereof. The selected genomic modifications provided herein enhance the therapeutic properties of the derivative cells. The derivative cells are functionally improved and suitable for allogeneic off- the-shelf cell therapies following a combination of selective modalities being introduced to the cells at the level of iPSC through genomic engineering. This approach can help to reduce the side effects mediated by CRS/GVHD and prevent long-term autoimmunity while providing excellent efficacy.
In accordance with the invention, the engineered iPSC’s hereof are capable of being differentiated into alpha beta T cell immune effector cells. As used herein, the term "differentiation" is the process by which an unspecialized ("uncommitted") or less specialized cell acquires the features of a specialized cell. Specialized cells include, for example, a blood cell or a muscle cell. A differentiated or differentiation- induced cell is one that has taken on a more specialized ("committed") position within the lineage of a cell. The term "committed", when applied to the process of differentiation, refers to a cell that has proceeded in the differentiation pathway to a point where, under normal circumstances, it will continue to differentiate into a specific cell type or subset of cell types, and cannot, under normal circumstances, differentiate into a different cell type or revert to a less differentiated cell type. As used herein, the term "pluripotent" refers to the ability of a cell to form all lineages of the body or soma or the embryo proper. For example, embryonic stem cells are a type of pluripotent stem cells that are able to form cells from each of the three germs layers, the ectoderm, the mesoderm, and the endoderm. Pluripotency is a continuum of developmental potencies ranging from the incompletely or partially pluripotent cell (e.g., an epiblast stem cell or EpiSC), which is unable to give rise to a complete organism to the more primitive, more pluripotent cell, which is able to give rise to a complete organism (e.g., an embryonic stem cell).
As used herein, the term "induced pluripotent stem cells" or, iPSCs, means that the stem cells are produced from differentiated adult, neonatal or fetal cells that have been induced or changed or reprogrammed into cells capable of differentiating into tissues of all three germ or dermal layers: mesoderm, endoderm, and ectoderm. The iPSCs produced do not refer to cells as they are found in nature.
As used herein, the terms "reprogramming" or "dedifferentiation" refers to a method of increasing the potency of a cell or dedifferentiating the cell to a less differentiated state. For example, a cell that has an increased cell potency has more developmental plasticity (i.e., can differentiate into more cell types) compared to the same cell in the non-reprogrammed state. In other words, a reprogrammed cell is one that is in a less differentiated state than the same cell in a non-reprogrammed state.
The term “hematopoietic stem and progenitor cells,” “hematopoietic stem cells,” “hematopoietic progenitor cells,” or “hematopoietic precursor cells” or “HPCs” refers to cells which are committed to a hematopoietic lineage but are capable of further hematopoietic differentiation. Hematopoietic stem cells include, for example, multipotent hematopoietic stem cells (hematoblasts), myeloid progenitors, megakaryocyte progenitors, erythrocyte progenitors, and lymphoid progenitors. Hematopoietic stem and progenitor cells (HSCs) are multipotent stem cells that give rise to all the blood cell types including myeloid (monocytes and macrophages, neutrophils, basophils, eosinophils, erythrocytes, megakaryocytes/platelets, dendritic cells), and lymphoid lineages (T cells, B cells, NK cells). As used herein, “CD34+ hematopoietic progenitor cell” refers to an HPC that expresses CD34 on its surface.
As used herein, the term “immune cell” or “immune effector cell” refers to a cell that is involved in an immune response. Immune response includes, for example, the promotion of an immune effector response. Examples of immune cells include T cells, B cells, natural killer (NK) cells, mast cells, and myeloid-derived phagocytes.
As used herein, the terms “T lymphocyte” and “T cell” are used interchangeably and refer to a type of white blood cell that completes maturation in the thymus and that has various roles in the immune system. A T cell can have the roles including, e.g., the identification of specific foreign antigens in the body and the activation and deactivation of other immune cells. A T cell can be any T cell, such as a cultured T cell, e.g., a primary T cell, or a T cell from a cultured T cell line, e.g., Jurkat, SupTl, etc., or a T cell obtained from a mammal. The T cell can be CD3+ cells. The T cell can be any type of T cell and can be of any developmental stage, including but not limited to, CD4+/CD8+ double positive T cells, CD4+ helper T cells (e.g., Thl and Th2 cells), CD8+ T cells (e.g., cytotoxic T cells), peripheral blood mononuclear cells (PBMCs), peripheral blood leukocytes (PBLs), tumor infiltrating lymphocytes (TILs), memory T cells, naive T cells, regulator T cells, gamma delta T cells (gd T cells), and the like. Additional types of helper T cells include cells such as Th3 (Treg), Thl7, Th9, or Tfh cells. Additional types of memory T cells include cells such as central memory T cells (Tcm cells), effector memory T cells (Tern cells and TEMRA cells). The T cell can also refer to a genetically engineered T cell, such as a T cell modified to express a T cell receptor (TCR) and/or a chimeric antigen receptor (CAR). The T cell can also be differentiated from a stem cell or progenitor cell.
“CD4+ T cells” refers to a subset of T cells that express CD4 on their surface and are associated with cell-mediated immune response. They are characterized by the secretion profiles following stimulation, which can include secretion of cytokines such as IFN-gamma, TNF-alpha, IL2, IL4 and IL10. “CD4” are 55-kD glycoproteins originally defined as differentiation antigens on T-lymphocytes, but also found on other cells including monocytes/macrophages. CD4 antigens are members of the immunoglobulin supergene family and are implicated as associative recognition elements in MHC (major histocompatibility complex) class Il-restricted immune responses. On T-lymphocytes they define the helper/inducer subset.
“CD8+ T cells” refers to a subset of T cells which express CD8 on their surface, are MHC class I-restricted, and function as cytotoxic T cells. “CD8” molecules are differentiation antigens found on thymocytes and on cytotoxic and suppressor T- lymphocytes. CD8 antigens are members of the immunoglobulin supergene family and are associative recognition elements in major histocompatibility complex class I-restricted interactions.
The induced pluripotent stem cell (iPSC) parental cell lines can be generated from peripheral blood mononuclear cells (PBMCs) or T cells using any known method for introducing re-programming factors into non-pluripotent cells using methods known in the art. For instance, the so called “Thompson Factors” as described in U.S. Pat. Nos. 8183038, 8268620, 8440461, 9499786, 10,865,381 can be used, or the Yamanaka Factors as described in U.S. Pat. No. 8,952,801 the complete disclosures of which are incorporated herein by reference. Methods include the episomal plasmid-based process as previously described in U.S. Pat. Nos. 8,546,140; 9,644,184; 9,328,332; and 8,765,470, as well as the Sendai virus and other methods as described by Malik, et al Methods Mol Biol. 2013 ; 997: 23-33, the complete disclosures of which are incorporated herein by reference. The reprogramming factors can be in a form of polynucleotides, and thus are introduced to the non-pluripotent cells by vectors such as a retrovirus, a Sendai virus, an adenovirus, an episome, and a mini-circle. In particular embodiments, the one or more polynucleotides encoding at least one reprogramming factor are introduced by a lentiviral vector. In some embodiments, the one or more polynucleotides introduced by an episomal vector. In various other embodiments, the one or more polynucleotides are introduced by a Sendai viral vector. In some embodiments, the iPSC’s are clonal iPSC’s or are obtained from a pool of iPSCs and the genome edits are introduced by making one or more targeted integration and/or in/del at one or more selected sites. In another embodiment, the iPSC’s are obtained from human T cells having antigen specificity and a reconstituted TCR gene (hereinafter, also referred to as "T-iPS” cells or “T-iPSC”) as described in US Pat. Nos. 9206394, and 10787642 hereby incorporated by reference into the present application. FIG. 1A-C show schematics of exemplary methods for generating iPSCs of the application.
As used herein, the term “genetic imprint” refers to genetic or epigenetic information that contributes to preferential therapeutic attributes in a source cell or an iPSC, and is retainable in the source cell derived iPSCs, and/or the iPSC-derived hematopoietic lineage cells. As used herein, “a source cell” is a non-pluripotent cell that can be used for generating iPSCs through reprogramming, and the source cell derived iPSCs can be further differentiated to specific cell types including any hematopoietic lineage cells. The source cell derived iPSCs, and differentiated cells therefrom are sometimes collectively called “derived” or “derivative” cells depending on the context. For example, derivative effector cells or derivative T or “iT” cells, as used throughout this application are cells differentiated from an iPSC, as compared to their primary counterpart obtained from natural/native sources such as peripheral blood, umbilical cord blood, or other donor tissues. As used herein, the genetic imprint(s) conferring a preferential therapeutic attribute is incorporated into the iPSCs either through reprogramming a selected source cell that is donor-, disease-, or treatment response- specific, or through introducing genetically modified modalities to iPSC using genomic editing.
In one general aspect, the application provides an induced pluripotent stem cell (iPSC) that comprises one or more polynucleotides encoding a rearranged ab TCR, wherein the rearranged ab TCR is a public TCR that specifically recognizes a non-human antigen in the context of a specific HLA class I (HLA-I) allele and wherein the rearranged ab TCR supports differentiation of the iPSC to a T cell.
I. TCR expression
A T cell receptor (TCR) is a membrane complex found on the surface of T cells that recognizes antigens specifically. It is a heterodimer consisting of alpha (a) and beta (b) chains or gamma (g) and delta (d) chains. Each of the alpha, beta, gamma and delta chains of a TCR can be a glycoprotein. As a member of the Ig superfamily, with Ig-like domains, a TCR generates its diversity in a manner similar to that for antibodies, e g., mainly from genetic recombination of the DNA-encoded segments in individual somatic T cells by somatic V(D)J recombination. In a single cell, the T cell receptor loci are rearranged and expressed stochastically. If both delta and gamma rearrangements produce functional polypeptides, the cell expresses delta and gamma. If not, the cell proceeds to rearrange the beta and alpha loci. However, unlike antibodies, TCR genes do not undergo somatic hypermutation. The TCRa gene locus contains variable (V) and joining (J) gene segments (nb and Ib), whereas the TCRb locus contains a D gene segment in addition to Va and Ja segments. Accordingly, the a chain is generated from VJ recombination and the b chain is generated involving VDJ recombination. Similarly, TCRy chain is generated involving VJ recombination and the TCR5 gene is generated involving VDJ recombination. The gene segments for TCR are flanked by the same recombination signal sequences as are the Ig gene segments, and the same RAG-1 and RAG-2 encoded recombinase and TdT are required for somatic recombination.
As used herein, a “rearranged TCR” is a TCR encoded by a rearranged TCR gene which has undergone a physical rearrangement whereby distant sub-genes are fused together. The human genome possesses four unique TCR gene clusters; alpha (a), beta (b), gamma (g), and delta (d), encoding the TCR alpha, beta, gamma and delta chains, respectively, via rearranged TCR genes. Each chain of the TCR has a variable and a constant region. The variable region contains three hypervariable or complementarity-determining regions (CDRs) and framework residues. CDR3, is mainly responsible for recognizing a processed antigen. To activate T cells, the TCR forms a molecular complex with the CD3 complex, which contains a CD3 gamma (g) chain, a CD3 delta (d) chain, two CD3 epsilon (e) chains, and two CD3 zeta (Q chains.
“Alpha-beta T cell receptors” or “ab TCR” are antigen specific T cell receptors essential to the immune response and have one a (alpha) chain and one b (beta) chain. Binding of ab TCR to peptide-major histocompatibility complex (pMHC) initiates TCR-CD3 intracellular activation, recruitment of numerous signaling molecules, and branching and integrating signaling pathways, leading to mobilization of transcription factors that are critical for gene expression and T cell growth and function acquisition. T cells with aB TCRs have specific reactivity to peptides presented via human leukocyte antigen (HLA) system or complex. HLA is the human nomenclature for MHC genes and proteins and can be used interchangeably (e.g. HLA-I is equivocal to MHC-I)
“HLA-restricted antigen recognition,” or “HLA restriction” refers to the fact that a T cell can recognize a foreign peptide bound to a self-major histocompatibility complex molecule, but will only respond to the antigen when it is bound to a particular HLA molecule (e.g., HLA- A*0201). During T cell development, T cells go through a selection process in the thymus to ensure that the TCR will not recognize HLA molecules presenting self-antigens. The selection process results in developed T cells with specific TCRs that only respond to certain HLA molecules but not others (e.g., non-restricted MHC molecules).
As used herein, a “public TCR” or “trusted TCR” is a TCR that comprises a sequence that occurs in multiple individuals with a certain HLA type. These sequences occur so frequently in people who carry the restricting HLA allele, that they have been proven in nature to be compatible with a vast diversity of HLA-I alleles. Thus, these TCRs fail to recognize non- restricted HLA molecules and are unlikely to participate in graft versus host disease. Public TCRs and methods of identifying them have been described by Choo et al., J Virol. 2014 Sep;88(18): 10613-23; Valkenburg et al., Proc Natl Acad Sci U S A. 2016 Apr 19; 113(16):4440- 5; Sant et al., Front Immunol. 2018 lun 27;9:1453; Chen et al., Cell Rep. 2017 Apr 18;19(3):569- 583; J Biol Chem. 2016 Nov 18;291(47):24335-24351; and Song et al., Nat Struct Mol Biol.
2017 Apr;24(4):395-406, the relevant disclosures of which are incorporated herein. The T cell receptor alpha locus (TRA) encodes the T cell receptor alpha chain. The human TRA locus is composed of 54 variable genes (TRAY) genes belonging to 41 subgroups, 61 joining segments (TRAJ), and a unique constant region (TRAC) gene. Several V genes of the alpha locus are known to be incapable of encoding a protein and are considered pseudogenes.
The TRA repertoire comprises 45-47 functional TRAV genes belonging to 33-35 subgroups, 50 functional TRAJ segments, and the unique TRAC gene. During T cell development, a recombination event occurs at the DNA level joining a V gene with a J segment, and the C gene is later joined by splicing at the RNA level. Recombination of different V gene segments with several J segments provides a range of antigen recognition. Additional diversity in antigen recognition is attained by junctional diversity, resulting from the random addition of nucleotides by terminal deoxynucleotidyl transferase. In certain embodiments, a polynucleotide encoding a a TCR chain comprises a a TCR variable gene selected from the group consisting of TRAV27 and TRAV13-1; an a TCRjoining gene selected from the group consisting of TRAJ41 and TRAJ37; and an a TCR constant gene TRAC.
T cell receptor beta locus (TRB) encodes the T cell receptor beta chain. The human TRB locus is composed of 39-46 functional TRBV genes belonging to 21-23 subgroups, two diversity regions (TRBD), thirteen joining segments (TRBJ), and two constant (TRBC) gene. In certain embodiments, a polynucleotide encoding a b TCR chain comprises a b chain variable gene TRBV19; a b chain variable gene selected from the group consisting of TRBJ2-7, TRBJ2-5, and TRBJ2-6; a b chain constant gene selected from the group consisting of TRBC 1 and TRBC2.
In certain embodiments, the rearranged ab TCR is endogenous to the ab T cell.
In certain embodiments, the rearranged ab TCR is recombinant.
In certain embodiments, the rearranged ab TCR enables increased expansion of the differentiated T cell after mitogenic stimulation than a T cell without the rearranged ab TCR.
In certain embodiments, the rearranged ab TCR binds to an antigen derived from a virus, bacteria, fungi or parasites. In certain embodiments, the rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza- A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
In certain embodiments, the rearranged ab TCR binds to an influenza peptide comprising the amino acid sequence of SEQ ID NO: 83. In certain embodiments, the rearranged ab TCR comprises an a TCR chain having a CDR3 of the amino acid sequence of SEQ ID NO: 84, and a b TCR chain having a CDR3 of the amino acid sequence of SEQ ID NO: 85.
In certain embodiments, the ab TCR comprises an a TCR chain comprising the amino acid sequence encoded by TRAV27 and TRAJ41 genes, and having the CDR3 of the amino acid sequence of SEQ ID NO: 84, and the b TCR chain comprising the amino acid sequence encoded by TRBV19 and TRBJ2-7 genes, and having the CDR3 of the amino acid sequence of SEQ ID NO: 85.
II. Chimeric antigen receptor (CAR)
According to embodiments of the application, an iPSC cell comprises (i) one or more polynucleotides encoding rearranged ab T cell receptor (TCR); and (ii) a polynucleotide encoding a chimeric antigen receptor (CAR), such as a CAR targeting a tumor antigen.
As used herein, the term “chimeric antigen receptor” (CAR) refers to a recombinant polypeptide comprising at least an extracellular domain that binds specifically to an antigen or a target, a transmembrane domain and an intracellular signaling domain. Engagement of the extracellular domain of the CAR with the target antigen on the surface of a target cell results in clustering of the CAR and delivers an activation stimulus to the CAR-containing cell. CARs redirect the specificity of immune effector cells and trigger proliferation, cytokine production, phagocytosis and/or production of molecules that can mediate cell death of the target antigenexpressing cell in a major histocompatibility (MHC)-independent manner.
As used herein, the term “signal peptide” refers to a leader sequence at the amino- terminus (N-terminus) of a nascent CAR protein, which co-translationally or post-translationally directs the nascent protein to the endoplasmic reticulum and subsequent surface expression.
As used herein, the term “extracellular antigen binding domain,” “extracellular domain,” or “extracellular ligand binding domain” refers to the part of a CAR that is located outside of the cell membrane and is capable of binding to an antigen, target or ligand.
As used herein, the term “hinge region” or “hinge domain” refers to the part of a CAR that connects two adjacent domains of the CAR protein, i.e., the extracellular domain and the transmembrane domain of the CAR protein.
As used herein, the term “transmembrane domain” refers to the portion of a CAR that extends across the cell membrane and anchors the CAR to cell membrane. As used herein, the term “intracellular signaling domain,” “cytoplasmic signaling domain,” or “intracellular signaling domain” refers to the part of a CAR that is located inside of the cell membrane and is capable of transducing an effector signal.
As used herein, the term “stimulatory molecule” refers to a molecule expressed by an immune cell (e.g., T cell) that provides the primary cytoplasmic signaling sequence(s) that regulate primary activation of receptors in a stimulatory way for at least some aspect of the immune cell signaling pathway. Stimulatory molecules comprise two distinct classes of cytoplasmic signaling sequence, those that initiate antigen-dependent primary activation (referred to as “primary signaling domains”), and those that act in an antigen-independent manner to provide a secondary of co-stimulatory signal (referred to as “co-stimulatory signaling domains”).
In certain embodiments, the extracellular domain comprises an antigen binding domain and/or an antigen binding fragment. The antigen binding fragment can, for example, be an antibody or antigen binding fragment thereof that specifically binds a tumor antigen. The antigen binding fragments of the application possess desirable functional properties, including but not limited to high-affinity binding to a tumor antigen.
As used herein, the term “antibody” is used in a broad sense and includes immunoglobulin or antibody molecules including human, humanized, composite and chimeric antibodies and antibody fragments that are monoclonal or polyclonal. In general, antibodies are proteins or peptide chains that exhibit binding specificity to a specific antigen. Antibody structures are well known. Immunoglobulins can be assigned to five major classes (i.e., IgA, IgD, IgE, IgG and IgM), depending on the heavy chain constant domain amino acid sequence. IgA and IgG are further sub-classified as the isotypes IgAl, IgA2, IgGl, IgG2, IgG3 and IgG4. Accordingly, the antibodies of the application can be of any of the five major classes or corresponding sub-classes. Preferably, the antibodies of the application are IgGl, IgG2, IgG3 or IgG4. Antibody light chains of vertebrate species can be assigned to one of two clearly distinct types, namely kappa and lambda, based on the amino acid sequences of their constant domains. Accordingly, the antibodies of the application can contain a kappa or lambda light chain constant domain. According to particular embodiments, the antibodies of the application include heavy and/or light chain constant regions from rat or human antibodies. In addition to the heavy and light constant domains, antibodies contain an antigen-binding region that is made up of a light chain variable region and a heavy chain variable region, each of which contains three domains (i.e., complementarity determining regions 1-3; CDR1, CDR2, and CDR3). The light chain variable region domains are alternatively referred to as LCDR1, LCDR2, and LCDR3, and the heavy chain variable region domains are alternatively referred to as HCDR1, HCDR2, and HCDR3.
As used herein, the term an “isolated antibody” refers to an antibody which is substantially free of other antibodies having different antigenic specificities (e.g., an isolated antibody that specifically binds to the specific tumor antigen is substantially free of antibodies that do not bind to the tumor antigen). In addition, an isolated antibody is substantially free of other cellular material and/or chemicals.
As used herein, the term “monoclonal antibody” refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that can be present in minor amounts. The monoclonal antibodies of the application can be made by the hybridoma method, phage display technology, single lymphocyte gene cloning technology, or by recombinant DNA methods. For example, the monoclonal antibodies can be produced by a hybridoma which includes a B cell obtained from a transgenic nonhuman animal, such as a transgenic mouse or rat, having a genome comprising a human heavy chain transgene and a light chain transgene.
As used herein, the term “antigen-binding fragment” refers to an antibody fragment such as, for example, a diabody, a Fab, a Fab', a F(ab')2, an Fv fragment, a disulfide stabilized Fv fragment (dsFv), a (dsFv)2, a bispecific dsFv (dsFv-dsFv1), a disulfide stabilized diabody (ds diabody), a single-chain antibody molecule (scFv), a single domain antibody (sdAb), a scFv dimer (bivalent diabody), a multispecific antibody formed from a portion of an antibody comprising one or more CDRs, a camelized single domain antibody, a minibody, a nanobody, a domain antibody, a bivalent domain antibody, a light chain variable domain (VL), a variable domain (VHH) of a camelid antibody, or any other antibody fragment that binds to an antigen but does not comprise a complete antibody structure. An antigen-binding fragment is capable of binding to the same antigen to which the parent antibody or a parent antibody fragment binds. As used herein, the term “single-chain antibody” refers to a conventional single-chain antibody in the field, which comprises a heavy chain variable region and a light chain variable region connected by a short peptide of about 15 to about 20 amino acids (e.g., a linker peptide).
As used herein, the term “single domain antibody” refers to a conventional single domain antibody in the field, which comprises a heavy chain variable region and a heavy chain constant region or which comprises only a heavy chain variable region.
As used herein, the term “human antibody” refers to an antibody produced by a human or an antibody having an amino acid sequence corresponding to an antibody produced by a human made using any technique known in the art. This definition of a human antibody includes intact or full-length antibodies, fragments thereof, and/or antibodies comprising at least one human heavy and/or light chain polypeptide.
As used herein, the term “humanized antibody” refers to a non-human antibody that is modified to increase the sequence homology to that of a human antibody, such that the antigenbinding properties of the antibody are retained, but its antigenicity in the human body is reduced.
As used herein, the term “chimeric antibody” refers to an antibody wherein the amino acid sequence of the immunoglobulin molecule is derived from two or more species. The variable region of both the light and heavy chains often corresponds to the variable region of an antibody derived from one species of mammal (e.g., mouse, rat, rabbit, etc.) having the desired specificity, affinity, and capability, while the constant regions correspond to the sequences of an antibody derived from another species of mammal (e.g., human) to avoid eliciting an immune response in that species.
As used herein, the term “multispecific antibody” refers to an antibody that comprises a plurality of immunoglobulin variable domain sequences, wherein a first immunoglobulin variable domain sequence of the plurality has binding specificity for a first epitope and a second immunoglobulin variable domain sequence of the plurality has binding specificity for a second epitope. In an embodiment, the first and second epitopes are on the same antigen, e.g., the same protein (or subunit of a multimeric protein). In an embodiment, the first and second epitopes overlap or substantially overlap. In an embodiment, the first and second epitopes do not overlap or do not substantially overlap. In an embodiment, the first and second epitopes are on different antigens, e.g., the different proteins (or different subunits of a multimeric protein). In an embodiment, a multispecific antibody comprises a third, fourth, or fifth immunoglobulin variable domain. In an embodiment, a multispecific antibody is a bispecific antibody molecule, a trispecific antibody molecule, or a tetraspecific antibody molecule.
As used herein, the term “bispecific antibody” refers to a multispecific antibody that binds no more than two epitopes or two antigens. A bispecific antibody is characterized by a first immunoglobulin variable domain sequence which has binding specificity for a first epitope and a second immunoglobulin variable domain sequence that has binding specificity for a second epitope. In an embodiment, the first and second epitopes are on the same antigen, e.g., the same protein (or subunit of a multimeric protein). In an embodiment, the first and second epitopes overlap or substantially overlap. In an embodiment, the first and second epitopes are on different antigens, e.g., the different proteins (or different subunits of a multimeric protein). In an embodiment, a bispecific antibody comprises a heavy chain variable domain sequence and a light chain variable domain sequence which have binding specificity for a first epitope and a heavy chain variable domain sequence and a light chain variable domain sequence which have binding specificity for a second epitope. In an embodiment, a bispecific antibody comprises a half antibody, or fragment thereof, having binding specificity for a first epitope and a half antibody, or fragment thereof, having binding specificity for a second epitope. In an embodiment, a bispecific antibody comprises a scFv, or fragment thereof, having binding specificity for a first epitope, and a scFv, or fragment thereof, having binding specificity for a second epitope. In an embodiment, a bispecific antibody comprises a VHH having binding specificity for a first epitope, and a VHH having binding specificity for a second epitope.
As used herein, an antigen binding domain or antigen binding fragment that “specifically binds to a tumor antigen” refers to an antigen binding domain or antigen binding fragment that binds a tumor antigen, with a KD of 1 x KG7 M or less, preferably 1 x 10 8 M or less, more preferably 5><10 9 M or less, H IO-9 M or less, 5xlO 10 M or less, or HIO-10 M or less. The term “KD” refers to the dissociation constant, which is obtained from the ratio of Kd to Ka (i.e., Kd/Ka) and is expressed as a molar concentration (M). KD values for antibodies can be determined using methods in the art in view of the present disclosure. For example, the KD of an antigen binding domain or antigen binding fragment can be determined by using surface plasmon resonance, such as by using a biosensor system, e.g., a Biacore® system, or by using bio-layer interferometry technology, such as an Octet RED96 system. The smaller the value of the KD of an antigen binding domain or antigen binding fragment, the higher affinity that the antigen binding domain or antigen binding fragment binds to a target antigen.
In various embodiments, antibodies or antibody fragments suitable for use in the CAR of the present disclosure include, but are not limited to, monoclonal antibodies, bispecific antibodies, multispecific antibodies, chimeric antibodies, polypeptide-Fc fusions, single-chain Fvs (scFv), single chain antibodies, Fab fragments, F(ab') fragments, disulfide-linked Fvs (sdFv), masked antibodies (e g., Probodies®), Small Modular ImmunoPharmaceuticals ("SMIPsTM"), intrabodies, minibodies, single domain antibody variable domains, nanobodies, VHHS, diabodies, tandem diabodies (TandAb®), anti -idiotypic (anti-id) antibodies (including, e.g., anti-id antibodies to antigen-specific TCR), and epitope-binding fragments of any of the above. Antibodies and/or antibody fragments can be derived from murine antibodies, rabbit antibodies, human antibodies, fully humanized antibodies, camelid antibody variable domains and humanized versions, shark antibody variable domains and humanized versions, and camelized antibody variable domains.
In some embodiments, the antigen-binding fragment is an Fab fragment, an Fab1 fragment, an F(ab')2 fragment, an scFv fragment, an Fv fragment, a dsFv diabody, a VHH, a VNAR, a single-domain antibody (sdAb) or nanobody, a dAb fragment, aFd' fragment, a Fd fragment, a heavy chain variable region, an isolated complementarity determining region (CDR), a diabody, a triabody, or a decabody. In some embodiments, the antigen-binding fragment is an scFv fragment.
In certain embodiments, the antigen binding domain of the CAR is a single-domain antibody (sdAb), also known as a nanobody, an antibody fragment consisting of a single monomeric variable antibody domain, including heavy-chain antibodies found in camelids; the so called VHH fragments. (Hamers-Casterman et al., Nature, 363, 446448 (1993); see also U.S. Pat. No. 5,759,808; U.S. Pat. No. 5,800,988; U.S. Pat. No. 5,840,526; and U.S. Pat. No. 5,874,541, hereby incorporated by reference). Cartilaginous fishes also have heavy-chain antibodies (IgNAR, 'immunoglobulin new antigen receptor'), from which single-domain antibodies called VNAR fragments can be obtained and these can be used in the invention. An alternative approach is to split the dimeric variable domains from common immunoglobulin G (IgG) from humans or mice into monomers. Although most research into single-domain antibodies is currently based on heavy chain variable domains, nanobodies derived from light chains have also been shown to bind specifically to target epitopes and can also be employed.
Alternative scaffolds to immunoglobulin domains that exhibit similar functional characteristics, such as high-affinity and specific binding of target biomolecules, can also be used in the CARs of the present disclosure. Such scaffolds have been shown to yield molecules with improved characteristics, such as greater stability or reduced immunogenicity. Non-limiting examples of alternative scaffolds that can be used in the CAR of the present disclosure include engineered, tenascin-derived, tenascin type III domain (e.g., Centyrin™); engineered, gamma-B crystallin-derived scaffold or engineered, ubiquitin-derived scaffold (e.g., Affilins); engineered, fibronectin-derived, 10th fibronectin type III (10Fn3) domain (e.g., monobodies, AdNectins™, or AdNexins™);; engineered, ankyrin repeat motif containing polypeptide (e.g., DARPins™); engineered, low-density -lipoprotein-receptor-derived, A domain (LDLR-A) (e.g., Avimers™); lipocalin (e.g., anticalins); engineered, protease inhibitor-derived, Kunitz domain (e.g., EETΊ- IEAGRP, BPTI/LACI-D1/ITI-D2); engineered, Protein-A-derived, Z domain (Affibodies™); Sac7d-derived polypeptides (e.g., Nanoffitins® or affitins); engineered, Fyn-derived, SH2 domain (e.g., Fynomers®); CTLD3 (e.g., Tetranectin); thioredoxin (e.g., peptide aptamer); KALBITOR®; the b-sandwich (e.g., iMab); miniproteins; C-type lectin-like domain scaffolds; engineered antibody mimics; and any genetically manipulated counterparts of the foregoing that retains its binding functionality (Worn A, Pluckthun A, J Mol Biol 305: 989-1010 (2001); Xu L et ah, Chem Biol 9: 933-42 (2002); Wikman M et al., Protein Eng Des Sel 17: 455-62 (2004); Binz H et al., Nat Biol echnol 23: 1257-68 (2005); Hey T et al., Trends Biotechnol 23:514-522 (2005); Holliger P, Hudson P, Nat Biotechnol 23: 1126-36 (2005); Gill D, Damle N, Curr Opin Biotech 17: 653-8 (2006); Koide A, Koide S, Methods Mol Biol 352: 95-109 (2007); Skerra, Current Opin. in Biotech., 2007 18: 295-304; Byla P et al., J Biol Chem 285: 12096 (2010); Zoller F et al., Molecules 16: 2467-85 (2011), each of which is incorporated by reference in its entirety).
In some embodiments, the alternative scaffold is Affilin or Centyrin.
In some embodiments, the first polypeptide of the CARs of the present disclosure comprises a leader sequence. The leader sequence can be positioned at the N-terminus the extracellular binding domain. The leader sequence can be optionally cleaved from the extracellular binding domain during cellular processing and localization of the CAR to the cellular membrane. Any of various leader sequences known to one of skill in the art can be used as the leader sequence. Non-limiting examples of peptides from which the leader sequence can be derived include granulocyte-macrophage colony-stimulating factor receptor (GMCSFR),
FccR, human immunoglobulin (IgG) heavy chain (HC) variable region, CD8a, or any of various other proteins secreted by T cells. In various embodiments, the leader sequence is compatible with the secretory pathway of a T cell. In certain embodiments, the leader sequence is derived from human immunoglobulin heavy chain (HC).
In some embodiments, the leader sequence is derived from GMCSFR. In one embodiment, the GMCSFR leader sequence comprises the amino acid sequence set forth in SEQ ID NO: 1, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 1.
In some embodiments, the first polypeptide of the CARs of the present disclosure comprise a transmembrane domain, fused in frame between the extracellular binding domain and the cytoplasmic domain.
The transmembrane domain can be derived from the protein contributing to the extracellular binding domain, the protein contributing the signaling or co-signaling domain, or by a totally different protein. In some instances, the transmembrane domain can be selected or modified by amino acid substitution, deletions, or insertions to minimize interactions with other members of the CAR complex. In some instances, the transmembrane domain can be selected or modified by amino acid substitution, deletions, or insertions to avoid binding of proteins naturally associated with the transmembrane domain. In certain embodiments, the transmembrane domain includes additional amino acids to allow for flexibility and/or optimal distance between the domains connected to the transmembrane domain.
The transmembrane domain can be derived either from a natural or from a synthetic source. Where the source is natural, the domain can be derived from any membrane-bound or transmembrane protein. Non-limiting examples of transmembrane domains of particular use in this disclosure can be derived from (i.e. comprise at least the transmembrane region(s) of) the a, b or z chain of the T cell receptor (TCR), CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD8a, CD9, CD 16, CD22, CD33, CD37, CD40, CD64, CD80, CD86, CD134, CD137, or CD154. Alternatively, the transmembrane domain can be synthetic, in which case it will comprise predominantly hydrophobic residues such as leucine and valine. For example, a triplet of phenylalanine, tryptophan and/or valine can be found at each end of a synthetic transmembrane domain.
In some embodiments, it will be desirable to utilize the transmembrane domain of the z, h or FccRly chains which contain a cysteine residue capable of disulfide bonding, so that the resulting chimeric protein will be able to form disulfide linked dimers with itself, or with unmodified versions of the z, h or FcsRly chains or related proteins. In some instances, the transmembrane domain will be selected or modified by amino acid substitution to avoid binding of such domains to the transmembrane domains of the same or different surface membrane proteins to minimize interactions with other members of the receptor complex. In other cases, it will be desirable to employ the transmembrane domain of z, h or FcsRly and -b, MB1 (Iga.), B29 or CD3- g, z, or h, in order to retain physical association with other members of the receptor complex.
In some embodiments, the transmembrane domain is derived from CD8 or CD28. In one embodiment, the CD8 transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 23, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 23. In one embodiment, the CD28 transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 24, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 24.
In some embodiments, the first polypeptide of the CAR of the present disclosure comprises a spacer region between the extracellular binding domain and the transmembrane domain, wherein the binding domain, linker, and the transmembrane domain are in frame with each other.
The term “spacer region” as used herein generally means any oligo- or polypeptide that functions to link the binding domain to the transmembrane domain. A spacer region can be used to provide more flexibility and accessibility for the binding domain. A spacer region can comprise up to 300 amino acids, preferably 10 to 100 amino acids and most preferably 25 to 50 amino acids. A spacer region can be derived from all or part of naturally occurring molecules, such as from all or part of the extracellular region of CD8, CD4 or CD28, or from all or part of an antibody constant region. Alternatively, the spacer region can be a synthetic sequence that corresponds to a naturally occurring spacer region sequence, or can be an entirely synthetic spacer region sequence. Non-limiting examples of spacer regions which can be used in accordance to the disclosure include a part of human CD8a chain, partial extracellular domain of CD28, FcyRllla receptor, IgG, IgM, IgA, IgD, IgE, an Ig hinge, or functional fragment thereof.
In some embodiments, additional linking amino acids are added to the spacer region to ensure that the antigen-binding domain is an optimal distance from the transmembrane domain. In some embodiments, when the spacer is derived from an Ig, the spacer can be mutated to prevent Fc receptor binding.
In some embodiments, the spacer region comprises a hinge domain. The hinge domain can be derived from CD8a, CD28, or an immunoglobulin (IgG). For example, the IgG hinge can be from IgGl, IgG2, IgG3, IgG4, IgMl, IgM2, IgAl, IgA2, IgD, IgE, or a chimera thereof.
In certain embodiments, the hinge domain comprises an immunoglobulin IgG hinge or functional fragment thereof. In certain embodiments, the IgG hinge is from IgGl, IgG2, IgG3, IgG4, IgMl, IgM2, IgAl, IgA2, IgD, IgE, or a chimera thereof. In certain embodiments, the hinge domain comprises the CHI, CH2, CH3 and/or hinge region of the immunoglobulin. In certain embodiments, the hinge domain comprises the core hinge region of the immunoglobulin. The term “core hinge” can be used interchangeably with the term “short hinge” (a.k.a. “SH”). Non-limiting examples of suitable hinge domains are the core immunoglobulin hinge regions include EPKSCDKTHTCPPCP (SEQ ID NO: 57) from IgGl, ERKCCVECPPCP (SEQ ID NO: 58) from IgG2, ELKTPLGDTTHTCPRCP(EPKSCDTPPPCPRCP)3 (SEQ ID NO: 59) from IgG3, and ESKYGPPCPSCP (SEQ ID NO: 60) from IgG4 (see also Wypych et al., JBC 2008 283(23): 16194-16205, which is incorporated herein by reference in its entirety for all purposes). In certain embodiments, the hinge domain is a fragment of the immunoglobulin hinge.
In some embodiments, the hinge domain is derived from CD8 or CD28. In one embodiment, the CD8 hinge domain comprises the amino acid sequence set forth in SEQ ID NO: 21, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 21. In one embodiment, the CD28 hinge domain comprises the amino acid sequence set forth in SEQ ID NO: 22, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 22.
In some embodiments, the transmembrane domain and/or hinge domain is derived from CD8 or CD28. In some embodiments, both the transmembrane domain and hinge domain are derived from CD8. In some embodiments, both the transmembrane domain and hinge domain are derived from CD28.
In certain aspects, the first polypeptide of CARs of the present disclosure comprise a cytoplasmic domain, which comprises at least one intracellular signaling domain. In some embodiments, cytoplasmic domain also comprises one or more co-stimulatory signaling domains.
The cytoplasmic domain is responsible for activation of at least one of the normal effector functions of the host cell (e g., T cell) in which the CAR has been placed in. The term “effector function” refers to a specialized function of a cell. Effector function of a T cell, for example, can be cytolytic activity or helper activity including the secretion of cytokines. Thus, the term “signaling domain” refers to the portion of a protein which transduces the effector function signal and directs the cell to perform a specialized function. While usually the entire signaling domain is present, in many cases it is not necessary to use the entire chain. To the extent that a truncated portion of the intracellular signaling domain is used, such truncated portion can be used in place of the intact chain as long as it transduces the effector function signal. The term intracellular signaling domain is thus meant to include any truncated portion of the signaling domain sufficient to transduce the effector function signal.
Non-limiting examples of signaling domains which can be used in the CARs of the present disclosure include, e g., signaling domains derived from DAP10, DAP12, Fc epsilon receptor I g chain (FCER1G), FcR b, CD36, CD3a, CD3y, Oϋ3z, CD2, CD5, CD22, CD226, CD66d, CD79A, and CD79B.
In some embodiments, the cytoplasmic domain comprises a Oϋ3z signaling domain. In one embodiment, the Oϋ3z signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 6, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 6. In some embodiments, the cytoplasmic domain further comprises one or more costimulatory signaling domains. In some embodiments, the one or more co-stimulatory signaling domains are derived from CD28, 4 IBB, IL2Rb, CD40, 0X40 (CD 134), CD80, CD86, CD27, ICOS, NKG2D, DAP 10, DAP 12, 2B4 (CD244), BTLA, CD30, GITR, CD226, CD79A, and HVEM.
In one embodiment, the co-stimulatory signaling domain is derived from 41BB. In one embodiment, the 4 IBB co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 8, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 8.
In one embodiment, the co-stimulatory signaling domain is derived from IL2Rb . In one embodiment, the IL2Rb co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 9, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 9.
In one embodiment, the co-stimulatory signaling domain is derived from CD40. In one embodiment, the CD40 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 10, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 10.
In one embodiment, the co-stimulatory signaling domain is derived from 0X40. In one embodiment, the 0X40 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 11, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 11.
In one embodiment, the co-stimulatory signaling domain is derived from CD80. In one embodiment, the CD80 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 12, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 12. In one embodiment, the co-stimulatory signaling domain is derived from CD86. In one embodiment, the CD86 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 13, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 13.
In one embodiment, the co-stimulatory signaling domain is derived from CD27. In one embodiment, the CD27 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 14, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 14.
In one embodiment, the co-stimulatory signaling domain is derived from ICOS. In one embodiment, the ICOS co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 15, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 15.
In one embodiment, the co-stimulatory signaling domain is derived from NKG2D. In one embodiment, the NKG2D co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 16, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 16.
In one embodiment, the co-stimulatory signaling domain is derived from DAPIO. In one embodiment, the DAPIO co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 17, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 17.
In one embodiment, the co-stimulatory signaling domain is derived from DAP 12. In one embodiment, the DAP12 co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 18, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 18. In one embodiment, the co-stimulatory signaling domain is derived from 2B4 (CD244).
In one embodiment, the 2B4 (CD244) co-stimulatory signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 19, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 19.
In some embodiments, the CAR of the present disclosure comprises one costimulatory signaling domains. In some embodiments, the CAR of the present disclosure comprises two or more costimulatory signaling domains. In certain embodiments, the CAR of the present disclosure comprises two, three, four, five, six or more costimulatory signaling domains. In some embodiments, the signaling domain(s) and costimulatory signaling domain(s) can be placed in any order. In some embodiments, the signaling domain is upstream of the costimulatory signaling domains. In some embodiments, the signaling domain is downstream from the costimulatory signaling domains. In the cases where two or more costimulatory domains are included, the order of the costimulatory signaling domains could be switched. Non-limiting exemplary CAR regions and sequences are provided in Table 1.
Table 1.
Figure imgf000041_0001
Figure imgf000042_0001
Figure imgf000043_0001
Figure imgf000044_0001
In some embodiments, the antigen-binding domain of the second polypeptide binds to an antigen. The antigen-binding domain of the second polypeptide can bind to more than one antigen or more than one epitope in an antigen. For example, the antigen-binding domain of the second polypeptide can bind to two, three, four, five, six, seven, eight or more antigens. As another example, the antigen-binding domain of the second polypeptide can bind to two, three, four, five, six, seven, eight or more epitopes in the same antigen.
The choice of antigen-binding domain may depend upon the type and number of antigens that define the surface of a target cell. For example, the antigen-binding domain can be chosen to recognize an antigen that acts as a cell surface marker on target cells associated with a particular disease state. In certain embodiments, the CARs of the present disclosure can be genetically modified to target a tumor antigen of interest by way of engineering a desired antigen-binding domain that specifically binds to an antigen (e.g., on a tumor cell). Non-limiting examples of cell surface markers that can act as targets for the antigen-binding domain in the CAR of the disclosure include those associated with tumor cells or autoimmune diseases.
In some embodiments, the antigen-binding domain binds to at least one tumor antigen or autoimmune antigen.
In some embodiments, the antigen-binding domain binds to at least one tumor antigen. In some embodiments, the antigen-binding domain binds to two or more tumor antigens. In some embodiments, the two or more tumor antigens are associated with the same tumor. In some embodiments, the two or more tumor antigens are associated with different tumors.
In some embodiments, the antigen-binding domain binds to at least one autoimmune antigen. In some embodiments, the antigen-binding domain binds to two or more autoimmune antigens. In some embodiments, the two or more autoimmune antigens are associated with the same autoimmune disease. In some embodiments, the two or more autoimmune antigens are associated with different autoimmune diseases.
In some embodiments, the tumor antigen is associated with glioblastoma, ovarian cancer, cervical cancer, head and neck cancer, liver cancer, prostate cancer, pancreatic cancer, renal cell carcinoma, bladder cancer, or hematologic malignancy. Non-limiting examples of tumor antigen associated with glioblastoma include HER2, EGFRvIII, EGFR, CD133, PDGFRA, FGFR1, FGFR3, MET, CD70, ROBOland IL13Ra2. Non-limiting examples of tumor antigens associated with ovarian cancer include FOLR1, FSHR, MUC16, MUC1, Mesothelin, CA125, EpCAM, EGFR, PDGFRa, Nectin-4, and B7H4. Non-limiting examples of the tumor antigens associated with cervical cancer or head and neck cancer include GD2, MUC1, Mesothelin, HER2, and EGFR. Non-limiting examples of tumor antigen associated with liver cancer include Claudin 18.2, GPC-3, EpCAM, cMET, and AFP. Non-limiting examples of tumor antigens associated with hematological malignancies include CD22, CD79 (CD79a and/or CD79b), BCMA, GPRC5D, SLAM F7, CD33, CLL1, CD123, and CD70. Non-limiting examples of tumor antigens associated with bladder cancer include Nectin-4 and SLITRK6.
Additional examples of antigens that can be targeted by the antigen-binding domain include, but are not limited to, alpha-fetoprotein, A3, antigen specific for A33 antibody, Ba 733, BrE3 -antigen, carbonic anhydrase EX, CD1, CDla, CD3, CD5, CD15, CD16, CD19, CD20, CD21, CD22, CD23, CD25, CD30, CD33, CD38, CD45, CD74, CD79a, CD80, CD123, CD138, colon-specific antigen-p (CSAp), CEA (CEACAM5), CEACAM6, CSAp, EGFR, EGP-I, EGP- 2, Ep-CAM, EphAl, EphA2, EphA3, EphA4, EphA5, EphA6, EphA7, EphA8, EphAlO, EphBl, EphB2, EphB3, EphB4, EphB6, FIt-I, Flt-3, folate receptor, HLA-DR, human chorionic gonadotropin (HCG) and its subunits, hypoxia inducible factor (HIF-I), la, IL-2, IL-6, IL-8, insulin growth factor-1 (IGF-I), KC4-antigen, KS-l-antigen, KS1-4, Le-Y, macrophage inhibition factor (MIF), MAGE, MUC2, MUC3, MUC4, NCA66, NCA95, NCA90, antigen specific for PAM-4 antibody, placental growth factor, p53, prostatic acid phosphatase, PSA, PSMA, RS5, SI 00, TAC, TAG-72, tenascin, TRAIL receptors, Tn antigen, Thomson- Friedenreich antigens, tumor necrosis antigens, VEGF, ED-B fibronectin, 17-lA-antigen, an angiogenesis marker, an oncogene marker or an oncogene product.
In one embodiment, the antigen targeted by the antigen-binding domain is CD19. In one embodiment, the antigen-binding domain comprises an anti-CD19 scFv. In one embodiment, the anti-CD 19 scFv comprises a heavy chain variable region (VH) comprising the amino acid sequence set forth in SEQ ID NO: 2, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 2. In one embodiment, the anti-CD 19 scFv comprises a light chain variable region (VL) comprising the amino acid sequence set forth in SEQ ID NO: 4, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 4. In one embodiment, the anti-CD19 scFv comprises the amino acid sequence set forth in SEQ ID NO: 7, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 7.
In some embodiments, the antigen is associated with an autoimmune disease or disorder. Such antigens can be derived from cell receptors and cells which produce “self ’-directed antibodies. In some embodiments, the antigen is associated with an autoimmune disease or disorder such as Rheumatoid arthritis (RA), multiple sclerosis (MS), Sjogren's syndrome, Systemic lupus erythematosus, sarcoidosis, Type 1 diabetes mellitus, insulin dependent diabetes mellitus (IDDM), autoimmune thyroiditis, reactive arthritis, ankylosing spondylitis, scleroderma, polymyositis, dermatomyositis, psoriasis, vasculitis, Wegener's granulomatosis, Myasthenia gravis, Hashimoto's thyroiditis, Graves' disease, chronic inflammatory demyelinating polyneuropathy, Guillain-Barre syndrome, Crohn's disease or ulcerative colitis.
In some embodiments, autoimmune antigens that can be targeted by the CAR disclosed herein include but are not limited to platelet antigens, myelin protein antigen, Sm antigens in snRNPs, islet cell antigen, Rheumatoid factor, and anticitrullinated protein citrullinated proteins and peptides such as CCP-1, CCP-2 (cyclical citrullinated peptides), fibrinogen, fibrin, vimentin, fillaggrin, collagen I and II peptides, alpha-enolase, translation initiation factor 4G1, perinuclear factor, keratin, Sa (cytoskeletal protein vimentin), components of articular cartilage such as collagen II, IX, and XI, circulating serum proteins such as RFs (IgG, IgM), fibrinogen, plasminogen, ferritin, nuclear components such as RA33/hnRNP A2, Sm, eukaryotic trasnlation elogation factor 1 alpha 1, stress proteins such as HSP-65, -70, -90, BiP, inflammatory /immune factors such as B7-H1, IL-1 alpha, and IL-8, enzymes such as calpastatin, alpha-enolase, aldolase- A, dipeptidyl peptidase, osteopontin, glucose-6-phosphate isomerase, receptors such as lipocortin 1, neutrophil nuclear proteins such as lactoferrin and 25-35 kD nuclear protein, granular proteins such as bactericidal permeability increasing protein (BPI), elastase, cathepsin G, myeloperoxidase, proteinase 3, platelet antigens, myelin protein antigen, islet cell antigen, rheumatoid factor, histones, ribosomal P proteins, cardiolipin, vimentin, nucleic acids such as dsDNA, ssDNA, and RNA, ribonuclear particles and proteins such as Sm antigens (including but not limited to SmD's and SmB'/B), U1RNP, A2/B1 hnRNP, Ro (SSA), and La (SSB) antigens.
In various embodiments, the scFv fragment used in the CAR of the present disclosure can include a linker between the VH and VL domains. The linker can be a peptide linker and can include any naturally occurring amino acid. Exemplary amino acids that can be included into the linker are Gly, Ser Pro, Thr, Glu, Lys, Arg, He, Leu, His and The. The linker should have a length that is adequate to link the VH and the VL in such a way that they form the correct conformation relative to one another so that they retain the desired activity, such as binding to an antigen. The linker can be about 5-50 amino acids long. In some embodiments, the linker is about 10-40 amino acids long. In some embodiments, the linker is about 10-35 amino acids long. In some embodiments, the linker is about 10-30 amino acids long. In some embodiments, the linker is about 10-25 amino acids long. In some embodiments, the linker is about 10-20 amino acids long. In some embodiments, the linker is about 15-20 amino acids long. Exemplary linkers that can be used are Gly rich linkers, Gly and Ser containing linkers, Gly and Ala containing linkers, Ala and Ser containing linkers, and other flexible linkers.
In one embodiment, the linker is a Whitlow linker. In one embodiment, the Whitlow linker comprises the amino acid sequence set forth in SEQ ID NO: 3, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 3. In another embodiment, the linker is a (GrS)3 linker. In one embodiment, the (G4S)3 linker comprises the amino acid sequence set forth in SEQ ID NO: 25, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 25.
Other linker sequences can include portions of immunoglobulin hinge area, CL or CHI derived from any immunoglobulin heavy or light chain isotype. Exemplary linkers that can be used include any of SEQ ID NOs: 26-56 in Table 1. Additional linkers are described for example in Int. Pat. Publ. No. W02019/060695, incorporated by reference herein in its entirety. III. Artificial Cell Death Polypeptide Safety Switch
According to certain embodiments of the application, an iPSC cell or a derivative cell thereof comprises an exogenous polynucleotide encoding an artificial cell death polypeptide.
As used herein, the term "an artificial cell death polypeptide" refers to an engineered protein designed to prevent potential toxicity or otherwise adverse effects of a cell therapy. The artificial cell death polypeptide could mediate induction of apoptosis, inhibition of protein synthesis, DNA replication, growth arrest, transcriptional and post-transcriptional genetic regulation and/or antibody -mediated depletion. In some instance, the artificial cell death polypeptide is activated by an exogenous molecule, e.g. an antibody, anti-viral drug, or radioisotopic conjugate drugs, that when activated, triggers apoptosis and/or cell death of a therapeutic cell. In certain embodiments, the mechanism of action of the artificial cell death polypeptide is metabolic, dimerization-inducing or therapeutic monoclonal antibody-mediated.
In certain embodiments, artificial cell death polypeptide is an inactivated cell surface receptor that comprises an epitope specifically recognized by an antibody, particularly a monoclonal antibody, which is also referred to herein as a monoclonal antibody-specific epitope. When expressed by iPSCs or derivative cells thereof, the inactivated cell surface receptor is signaling inactive or significantly impaired, but can still be specifically recognized by an antibody. The specific binding of the antibody to the inactivated cell surface receptor enables the elimination of the iPSCs or derivative cells thereof by ADCC and/or ADCP mechanisms, as well as, direct killing with antibody drug conjugates with toxins or radionuclides.
In certain embodiments, the inactivated cell surface receptor comprises an epitope that is selected from epitopes specifically recognized by an antibody, including but not limited to, ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, polatuzumab vedotin, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimumab, belimumab, canakinumab, denosumab, golimumab, ipilimumab, ofatumumab, panitumumab, or ustekinumab. Epidermal growth factor receptor, also known as EGFR, ErbBl and HER1, is a cell- surface receptor for members of the epidermal growth factor family of extracellular ligands. As used herein, “truncated EGFR,” “tEGFR,” “short EGFR” or “sEGFR” refers to an inactive EGFR variant that lacks the EGF-binding domains and the intracellular signaling domains of the EGFR. An exemplary tEGFR variant contains residues 322-333 of domain 2, all of domains 3 and 4 and the transmembrane domain of the native EGFR sequence containing the cetuximab binding epitope. Expression of the tEGFR variant on the cell surface enables cell elimination by an antibody that specifically binds to the tEGFR, such as cetuximab (Erbitux®), as needed. Due to the absence of the EGF-binding domains and intracellular signaling domains, tEGFR is inactive when expressed by iPSCs or derivative cell thereof.
An exemplary inactivated cell surface receptor of the application comprises a tEGFR variant. In certain embodiments, expression of the inactivated cell surface receptor in an engineered immune cell expressing a chimeric antigen receptor (CAR) induces cell suicide of the engineered immune cell when the cell is contacted with an anti-EGFR antibody. Methods of using inactivated cell surface receptors are described in W02019/070856, WO2019/023396, WO2018/058002, the disclosure of which is incorporated herein by reference. For example, a subject who has previously received an engineered immune cell of the present disclosure that comprises a heterologous polynucleotide encoding an inactivated cell surface receptor comprising a tEGFR variant can be administered an anti-EGFR antibody in an amount effective to ablate in the subject the previously administered engineered immune cell.
In certain embodiments, the anti-EGFR antibody is cetuximab, matuzumab, necitumumab or panitumumab, preferably the anti-EGFR antibody is cetuximab.
In certain embodiments, the tEGFR variant comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 71, preferably the amino acid sequence of SEQ ID NO: 71.
In some embodiments, the inactivated cell surface receptor comprises one or more epitopes of CD79b, such as an epitope specifically recognized by polatuzumab vedotin. In certain embodiments, the CD79b epitope comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 78, preferably the amino acid sequence of SEQ ID NO: 78. In some embodiments, the inactivated cell surface receptor comprises one or more epitopes of CD20, such as an epitope specifically recognized by rituximab. In certain embodiments, the CD20 epitope comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 80, preferably the amino acid sequence of SEQ ID NO: 80.
In some embodiments, the inactivated cell surface receptor comprises one or more epitopes of Her 2 receptor or ErbB, such as an epitope specifically recognized by trastuzumab. In certain embodiments, the monoclonal antibody-specific epitope comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 82, preferably the amino acid sequence of SEQ ID NO: 82.
In some embodiments the inactivated cell surface receptor further comprises a cytokine.
In some embodiments, an inactivated cell surface receptor further comprises a hinge domain. In some embodiments, the hinge domain is derived from CD8. In one embodiment, the CD8 hinge domain comprises the amino acid sequence set forth in SEQ ID NO: 21, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 21.
In certain embodiments, an inactivated cell surface receptor further comprises a transmembrane domain. In some embodiments, the transmembrane domain is derived from CD8. In one embodiment, the CD8 transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 23, or a variant thereof having at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 96, at least 97, at least 98 or at least 99%, sequence identity with SEQ ID NO: 23.
In certain embodiment, an inactivated cell surface receptor comprises one or more epitopes specifically recognized by an antibody in its extracellular domain, a transmembrane region and a cytoplasmic domain. In some embodiments, the inactivated cell surface receptor further comprises a hinge region between the epitope(s) and the transmembrane region. In some embodiments, the inactivated cell surface receptor comprises more than one epitopes specifically recognized by an antibody, the epitopes can have the same or different amino acid sequences, and the epitopes can be linked together via a peptide linker, such as a flexible peptide linker have the sequence of (GGGGS)n, wherein n is an integer of 1-8 (SEQ ID NO: 25). In some embodiments, the inactivated cell surface receptor further comprises a cytokine. In certain embodiments, the cytokine is in the cytoplasmic domain of the inactivated cell surface receptor. Preferably, the cytokine is operably linked to the epitope(s) specifically recognized by an antibody, directly or indirectly, via an autoprotease peptide sequence, such as those described herein. In some embodiments, the cytokine is indirectly linked to the epitope(s) by connecting to the transmembrane region via the autoprotease peptide sequence.
In other embodiments, the artificial cell death polypeptide is a viral enzyme that is recognized by an antiviral drug. In certain embodiments, the viral enzyme is a herpes simplex virus thymidine kinase (HSV-tk). In certain embodiments, the HSV-tk comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 96, preferably the amino acid sequence of SEQ ID NO: 96. This enzyme phosphorylates the nontoxic prodrug ganciclovir, which then becomes phosphorylated by endogenous kinases to GCV-triphosphate, causing chain termination and single-strand breaks upon incorporation into DNA, thereby killing dividing cells. In certain embodiments, expression of the viral enzyme in an engineered immune cell expressing a chimeric antigen receptor (CAR) induces cell death of the engineered immune cell when the cell is contacted with an antiviral drug. In certain embodiments, the antiviral drug is ganciclovir.
In certain embodiments, the artificial cell death polypeptide comprises an antigen targeted by a small molecule compound. In certain embodiments, the antigen is a truncated prostate-specific membrane antigen (PSMA) polypeptide as described in Inti. Pat. Applications WO2015143029A1 and WO2018187791A1, the disclosures of which are incorporated by reference into the present application in entirety. In certain embodiments, the prostate-specific membrane antigen (PSMA) polypeptide comprises or consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 97, preferably the amino acid sequence of SEQ ID NO: 97. In certain embodiments, expression of truncated PSMA in an engineered immune cell expressing a chimeric antigen receptor (CAR) induces cell death of the engineered immune cell when the cell is contacted with a radioisotopic conjugate drug that binds to PSMA via a small peptide. PSMA- targeting compounds are described in W02010/108125, the disclosure of which is incorporated herein by reference. In certain embodiments, the artificial cell death polypeptide comprises a herpes simplex virus thymidine kinase (HSV-tk) fused to a prostate-specific membrane antigen (PSMA) polypeptide via a linker. In certain embodiments, the linker comprises an amino acid sequence of SEQ ID NO: 48. In certain embodiments, the artificial cell death polypeptide comprises an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 98, preferably the amino acid sequence of SEQ ID NO: 98.
In certain embodiments, the artificial cell death polypeptide comprises a herpes simplex virus thymidine kinase (HSV-tk) and a prostate-specific membrane antigen (PSMA) polypeptide operably linked by an autoprotease peptide sequence. In certain embodiments, the autoprotease peptide is a thosea asigna virus 2A (T2A) peptide. In certain embodiments, the artificial cell death polypeptide comprises an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 99, preferably the amino acid sequence of SEQ ID NO: 99.
In certain embodiments, the artificial polypeptide comprises a prostate-specific membrane antigen (PSMA) polypeptide and a cluster of differentiation 24 (CD24) polypeptide operably linked by an autoprotease peptide sequence. In certain embodiments, the autoprotease peptide is a thosea asigna virus 2A (T2A) peptide. In certain embodiments, the artificial cell death polypeptide comprises an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 100, preferably the amino acid sequence of SEQ ID NO: 100.
IV. HLA
In one aspect, MHC I and/or MHC II knock-out and/or knock down can be incorporated in the cells for use in “allogeneic” cell therapies, in which cells are harvested from a subject, modified to knock-out or knock-down, e.g., disrupt, B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP gene expression, and then returned to a different subject. Knocking out or knocking down the B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes as described herein can: (1) prevent GvH response; (2) prevent HvG response; and/or (3) improve T cell safety and efficacy. Accordingly, in certain embodiments, a presently disclosed invention comprises independently knocking out and/or knocking down one or more genes selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes in a T cell. In certain embodiments, a presently disclosed method comprises independently knocking out and/or knocking down two genes selected from the group consisting B2M, TAP 1, TAP 2, Tapasin, RFXANK, CUT A, RFX5 and RFXAP genes in a T cell, in particular, B2M and CIITA to achieve class I and II HLA disruption.. In certain embodiments, an iPSC or derivative cell thereof of the application can be further modified by introducing an exogenous polynucleotide encoding one or more proteins related to immune evasion, such as non-classical HLA class I proteins (e.g., HLA-E and HLA-G). In particular, disruption of the B2M gene eliminates surface expression of all MHC class I molecules, leaving cells vulnerable to lysis by NK cells through the “missing self’ response. Exogenous HLA-E expression can lead to resistance to NK-mediated lysis (Gornalusse et ah, Nat Biotechnol. 2017; 35(8): 765-772).
In certain embodiments, the iPSC or derivative cell thereof comprises an exogenous polypeptide encoding at least one of a human leukocyte antigen E (HLA-E) and human leukocyte antigen G (HLA-G). In a particular embodiment, the HLA-E comprises an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 65, preferably the amino acid sequence of SEQ ID NO: 65. In a particular embodiment, the HLA-G comprises an amino acid sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 68, preferably SEQ ID NO: 68.
In certain embodiments, the exogenous polynucleotide encodes a polypeptide comprising a signal peptide operably linked to a mature B2M protein that is fused to an HLA-E via a linker. In a particular embodiment, the exogenous polypeptide comprises an amino acid sequence at least sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 66.
In other embodiments, the exogenous polynucleotide encodes a polypeptide comprising a signal peptide operably linked to a mature B2M protein that is fused to an HLA-G via a linker.
In a particular embodiment, the exogenous polypeptide comprises an amino acid sequence at least sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 69.
V. Other Optional Genome Edits
In certain embodiments, a cell of the application further comprises an exogenous polynucleotide encoding interleukin 15 (IL-15) and/or interleukin (IL-15) receptor or a variant or truncation thereof. As used herein “Interleukin- 15” or “IL-15” refers to a cytokine that regulates T and NK cell activation and proliferation. A “functional portion” (“biologically active portion”) of IL-15 refers to a portion of IL-15 that retains one or more functions of full length or mature IL-15. Such functions include the promotion of NK cell survival, regulation of NK cell and T cell activation and proliferation as well as the support of NK cell development from hematopoietic stem cells. As will be appreciated by those of skill in the art, the sequence of a variety of IL-15 molecules are known in the art. In certain embodiments, the IL-15 is a wild-type IL-15. In certain embodiments, the IL-15 is a human IL-15.
In another embodiment, the cell of the application further comprises an exogenous polynucleotide encoding a non-naturally occurring variant of FcyRIII (CD 16), for example, hnCD16 (see, e.g., Zhu et ah, Blood 2017, 130:4452, the contents of which are incorporated herein in their entirety by reference). As used herein, the term "hnCD16a" refers to a high affinity, non-cleavable variant of CD 16 (a low-affinity Fey receptor involved in antibody- dependent cellular cytotoxicity (ADCC). Typically, CD16 is cleaved during ADCC by proteases, whereas the hnCD16 CAR does not undergo this cleavage and thus sustains an ADCC signal longer. In some embodiments, the hnCD 16 is as disclosed in Blood 2016 128:3363, the entire contents of which is expressly incorporated herein by reference.
In another embodiment, a cell of the application further comprises an exogenous polynucleotide encoding interleukin 12 (IL-12) or interleukin 21 (IL-21) or a variant thereof.
In another embodiment, a cell of the application further comprises an exogenous polynucleotide encoding leukocyte surface antigen cluster of differentiation CD47 (CD47) as an NK inhibitory modality to overcome host-versus-graft immunoreactivity for allogeneic applications. As used herein, the term "CD47," also sometimes referred to as "integrin associated protein" (LAP), refers to a transmembrane protein that in humans is encoded by the CD47gene. CD47 belongs to the immunoglobulin superfamily, partners with membrane integrins, and also binds the ligands thrombospondin- 1 (TSP-1) and signal-regulatory protein alpha (SIRPa). CD47 acts as a signal to macrophages that allows CD47-expressing cells to escape macrophage attack. See, e.g., Deuse-T, et ah, Nature Biotechnology 201937: 252-258, the entire contents of which are incorporated herein by reference.
In another embodiment, a cell of the application further comprises an exogeneous polynucleotide encoding a constitutively active IL-7 receptor or variant thereof. IL-7 has a critical role in the development and maturation of T cells. It promotes the generation of naive and central memory T cell subsets and regulates their homeostasis. It has previously been reported that IL-7 prolonged the survival time of tumor-specific T cells in vivo. Cancer Medicine. 2014;3(3):550— 554. In previous studies, it has been reported that a constitutively activated IL-7 receptor (C7R) could result in IL-7 signaling in the absence of a ligand or with the existence of gamma chain (yc) of a coreceptor. Shum et al, Cancer Discovery. 2017;7(11): 1238— 1247. Insertion of a transmembrane domain such as cysteine and/or proline resulted in the homodimerization of IL-7Ra . Upon the formation of a homodimer, cross-phosphorylation of JAK1/JAK1 activates STAT5, thereby activating the downstream signaling of IL-7. Constructs for such constitutively activated IL-7 receptor (C7R) compositions are disclosed in WO2018/038945, the contents of which are hereby incorporated by reference into the present application.
In another embodiment, a cell of the application further comprises an exogenous polynucleotide encoding one or more imaging or reporter proteins, such as PSMA or HSV-tk.
For example, the cell can contain an exogeneous polynucleotide encoding prostate-specific membrane antigen (PSMA) as an imaging reporter in accordance with the disclosures of WO2015/ 143029 and WO2018/187791, the disclosures of which are incorporated herein by reference.
In one embodiment of the above described cell, the genomic editing at one or more selected sites can comprise insertions of one or more exogenous polynucleotides encoding other additional artificial cell death polypeptides proteins, targeting modalities, receptors, signaling molecules, transcription factors, pharmaceutically active proteins and peptides, drug target candidates, or proteins promoting engraftment, trafficking, homing, viability, self-renewal, persistence, and/or survival of the genome-engineered iPSCs or derivative cells thereof.
In some embodiments, the exogenous polynucleotides for insertion are operatively linked to (1) one or more exogenous promoters comprising CMV, EFla, PGK, CAG, UBC, or other constitutive, inducible, temporal-, tissue-, or cell type-specific promoters; or (2) one or more endogenous promoters comprised in the selected sites comprising AAVS1, CCR5, ROSA26, collagen, HTRP, HI, beta-2 microglobulin, GAPDH, TCR or RUNX1, or other locus meeting the criteria of a genome safe harbor. In some embodiments, the genome-engineered iPSCs generated using the above method comprise one or more different exogenous polynucleotides encoding proteins comprising caspase, thymidine kinase, cytosine deaminase, B-cell CD20, ErbB2 or CD79b wherein when the genome-engineered iPSCs comprise two or more suicide genes, the suicide genes are integrated in different safe harbor locus comprising AAVS1, CCR5, ROSA26, collagen, HTRP, Hll, HU, beta-2 microglobulin, GAPDH, TCR or RUNX1. Other exogenous polynucleotides encoding proteins can include those encoding PET reporters, homeostatic cytokines, and inhibitory checkpoint inhibitory proteins such as PD1, PD-L1, and CTLA4 as well as proteins that target the CD47/signal regulatory protein alpha (SIRPa) axis . In some other embodiments, the genome-engineered iPSCs generated using the method provided herein comprise in/del at one or more endogenous genes associated with targeting modality, receptors, signaling molecules, transcription factors, drug target candidates, immune response regulation and modulation, or proteins suppressing engraftment, trafficking, homing, viability, self-renewal, persistence, and/or survival of the iPSCs or derivative cells thereof.
In addition, the modified ab T cells can exhibit one or more edits in their genome that results in a loss-of-function in a target gene. A loss-of-function of a target gene is characterized by a decrease in the expression of a target gene based on a genomic modification, e.g., an RNA- guided nuclease-mediated cut in the target gene that results in an inactivation, or in diminished expression or function, of the encoded gene product. Examples of genes that can be targeted for loss of function include B2M, PD-1, CISH, CIITA, HLA class II histocompatibility alpha chain genes (e g HLA-DQA1, HLA-DRA, HLA-DPA1, HLA-DMA- HLA-DQA2 and or HLA- DOA), HLA Class II histocompatabilty beta chain genes (e.g. HLA-DMB,HLA-DOB, HLA- DPB1, HLA-DQB1, HLA-DQB2, HLA-DQB3, HLA-DRBl, HLADRB3, HLA-DRB4, and/or HLA-DRB5), CD32B, CTLA4, NKG2A, BIM, CCR5,CCR7, CD96, CDK8, CXCR3, EP4 (PGE2 RECEPTOR), Fas, GITR, IL1R8, KIRDLl, KIR2DL1-3, LAG3, SOCS genes, Sortilin, TIM3, TRAC, RAG1, RAG2 and NLRC5.
The modified cells of the application can exhibit any of the edits described, as well as any combination of such edits described.
VI. Targeted Genome Editing at Selected Locus in iPSCs
According to embodiments of the application, one or more of the exogenous polynucleotides are integrated at one or more loci on the chromosome of an iPSC.
Genome editing, or genomic editing, or genetic editing, as used interchangeably herein, is a type of genetic engineering in which DNA is inserted, deleted, and/or replaced in the genome of a targeted cell. Targeted genome editing (interchangeable with “targeted genomic editing” or “targeted genetic editing”) enables insertion, deletion, and/or substitution at pre-selected sites in the genome. When an endogenous sequence is deleted or dismpted at the insertion site during targeted editing, an endogenous gene comprising the affected sequence can be knocked-out or knocked-down due to the sequence deletion or disruption. Therefore, targeted editing can also be used to disrupt endogenous gene expression with precision. Similarly used herein is the term “targeted integration,” referring to a process involving insertion of one or more exogenous sequences at pre-selected sites in the genome, with or without deletion of an endogenous sequence at the insertion site.
Targeted editing can be achieved either through a nuclease-independent approach, or through a nuclease-dependent approach. In the nuclease-independent targeted editing approach, homologous recombination is guided by homologous sequences flanking an exogenous polynucleotide to be inserted, through the enzymatic machinery of the host cell.
Alternatively, targeted editing could be achieved with higher frequency through specific introduction of double strand breaks (DSBs) by specific rare-cutting endonucleases. Such nuclease-dependent targeted editing utilizes DNA repair mechanisms including non-homologous end joining (NHEJ), which occurs in response to DSBs. Without a donor vector containing exogenous genetic material, the NHEJ often leads to random insertions or deletions (in/dels) of a small number of endogenous nucleotides. In comparison, when a donor vector containing exogenous genetic material flanked by a pair of homology arms is present, the exogenous genetic material can be introduced into the genome during homology directed repair (HDR) by homologous recombination, resulting in a “targeted integration.”
Available endonucleases capable of introducing specific and targeted DSBs include, but not limited to, zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and, RNA-guided CRISPR (Clustered Regular Interspaced Short Palindromic Repeats) systems. Additionally, DICE (dual integrase cassette exchange) system utilizing phiC31 and Bxbl integrases is also a promising tool for targeted integration.
ZFNs are targeted nucleases comprising a nuclease fused to a zinc finger DNA binding domain. By a “zinc finger DNA binding domain” or “ZFBD” it is meant a polypeptide domain that binds DNA in a sequence-specific manner through one or more zinc fingers. A zinc finger is a domain of about 30 amino acids within the zinc finger binding domain whose structure is stabilized through coordination of a zinc ion. Examples of zinc fingers include, but not limited to, C2H2 zinc fingers, C3H zinc fingers, and C4 zinc fingers. A “designed” zinc finger domain is a domain not occurring in nature whose design/composition results principally from rational criteria, e.g., application of substitution rules and computerized algorithms for processing information in a database storing information of existing ZFP designs and binding data. See, for example, U.S. Pat. Nos. 6,140,081; 6,453,242; and 6,534,261; see also WO 98/53058; WO 98/53059; WO 98/53060; WO 02/016536 and WO 03/016496. A “selected” zinc finger domain is a domain not found in nature whose production results primarily from an empirical process such as phage display, interaction trap or hybrid selection. ZFNs are described in greater detail in U.S. Pat. No. 7,888,121 and U.S. Pat. No. 7,972,854, the complete disclosures of which are incorporated herein by reference. The most recognized example of a ZFN in the art is a fusion of the Fokl nuclease with a zinc finger DNA binding domain.
A TALEN is a targeted nuclease comprising a nuclease fused to a TAL effector DNA binding domain. By “transcription activator-like effector DNA binding domain”, “TAL effector DNA binding domain”, or “TALE DNA binding domain” it is meant the polypeptide domain of TAL effector proteins that is responsible for binding of the TAL effector protein to DNA. TAL effector proteins are secreted by plant pathogens of the genus Xanthomonas during infection. These proteins enter the nucleus of the plant cell, bind effector-specific DNA sequences via their DNA binding domain, and activate gene transcription at these sequences via their transactivation domains. TAL effector DNA binding domain specificity depends on an effector-variable number of imperfect 34 amino acid repeats, which comprise polymorphisms at select repeat positions called repeat variable-diresidues (RVD). TALENs are described in greater detail in U.S. Patent Application No. 2011/0145940, which is herein incorporated by reference. The most recognized example of a TALEN in the art is a fusion polypeptide of the Fokl nuclease to a TAL effector DNA binding domain.
Additional examples of targeted nucleases suitable for the present application include, but not limited to Spol 1, Bxbl, phiC3 1, R4, PhiBTl, and Wp/SPBc/TP901-l, whether used individually or in combination.
Other non-limiting examples of targeted nucleases include naturally occurring and recombinant nucleases; CRISPR related nucleases from families including cas, cpf, cse, csy, csn, csd, cst, csh, csa, csm, and cmr; restriction endonucleases; meganucleases; homing endonucleases, and the like. As an example, CRISPR/Cas9 requires two major components: (1) a Cas9 endonuclease and (2) the crRNA-tracrRNA complex. When co-expressed, the two components form a complex that is recruited to a target DNA sequence comprising PAM and a seeding region near PAM. The crRNA and tracrRNA can be combined to form a chimeric guide RNA (gRNA) to guide Cas9 to target selected sequences. These two components can then be delivered to mammalian cells via transfection or transduction. As another example,
CRISPR/Cpfl comprises two major components: (1) a CPfl endonuclease and (2) a crRNA. When co-expressed, the two components form a ribobnucleoprotein (RNP) complex that is recruited to a target DNA sequence comprising PAM and a seeding region near PAM. The crRNA can be combined to form a chimeric guide RNA (gRNA) to guide Cpfl to target selected sequences. These two components can then be delivered to mammalian cells via transfection or transduction.
MAD7 is an engineered Casl2a variant originating from the bacterium E bacterium rectale that has a preference for 5'-TTTN-3' and 5'-CTTN-3' PAM sites and does not require a tracrRNA. See, for example, PCT Publication No. 2018/236548, the disclosure of which is incorporated herein by reference.
DICE mediated insertion uses a pair of recombinases, for example, phiC31 and Bxbl, to provide unidirectional integration of an exogenous DNA that is tightly restricted to each enzymes’ own small attB and attP recognition sites. Because these target att sites are not naturally present in mammalian genomes, they must be first introduced into the genome, at the desired integration site. See, for example, U.S. Application Publication No. 2015/0140665, the disclosure of which is incorporated herein by reference.
One aspect of the present application provides a construct comprising one or more exogenous polynucleotides for targeted genome integration. In one embodiment, the construct further comprises a pair of homologous arm specific to a desired integration site, and the method of targeted integration comprises introducing the construct to cells to enable site specific homologous recombination by the cell host enzymatic machinery. In another embodiment, the method of targeted integration in a cell comprises introducing a construct comprising one or more exogenous polynucleotides to the cell, and introducing a ZFN expression cassette comprising a DNA-binding domain specific to a desired integration site to the cell to enable a ZFN-mediated insertion. In yet another embodiment, the method of targeted integration in a cell comprises introducing a construct comprising one or more exogenous polynucleotides to the cell, and introducing a TALEN expression cassette comprising a DNA-binding domain specific to a desired integration site to the cell to enable a TALEN-mediated insertion. In another embodiment, the method of targeted integration in a cell comprises introducing a construct comprising one or more exogenous polynucleotides to the cell, introducing a Cpfl expression cassette, and a gRNA comprising a guide sequence specific to a desired integration site to the cell to enable a Cpfl -mediated insertion. In another embodiment, the method of targeted integration in a cell comprises introducing a construct comprising one or more exogenous polynucleotides to the cell, introducing a Cas9 expression cassette, and a gRNA comprising a guide sequence specific to a desired integration site to the cell to enable a Cas9-mediated insertion. In still another embodiment, the method of targeted integration in a cell comprises introducing a construct comprising one or more att sites of a pair of DICE recombinases to a desired integration site in the cell, introducing a construct comprising one or more exogenous polynucleotides to the cell, and introducing an expression cassette for DICE recombinases, to enable DICE-mediated targeted integration.
Sites for targeted integration include, but are not limited to, genomic safe harbors, which are intragenic or extragenic regions of the human genome that, theoretically, are able to accommodate predictable expression of newly integrated DNA without adverse effects on the host cell or organism. In certain embodiments, the genome safe harbor for the targeted integration is one or more loci of genes selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, HU, GAPDH, TCR and RUNX1 genes.
In other embodiments, the site for targeted integration is selected for deletion or reduced expression of an endogenous gene at the insertion site. As used herein, the term “deletion” with respect to expression of a gene refers to any genetic modification that abolishes the expression of the gene. Examples of “deletion” of expression of a gene include, e.g., a removal or deletion of a DNA sequence of the gene, an insertion of an exogenous polynucleotide sequence at a locus of the gene, and one or more substitutions within the gene, which abolishes the expression of the gene.
Genes for target deletion include, but are not limited to, genes of major histocompatibility complex (MHC) class I and MHC class II proteins. Multiple MHC class I and class II proteins must be matched for histocompatibility in allogeneic recipients to avoid allogeneic rejection problems. “MHC deficient”, including MHC-class I deficient, or MHC-class II deficient, or both, refers to cells that either lack, or no longer maintain, or have reduced level of surface expression of a complete MHC complex comprising a MHC class I protein heterodimer and/or a MHC class II heterodimer, such that the diminished or reduced level is less than the level naturally detectable by other cells or by synthetic methods. MHC class I deficiency can be achieved by functional deletion of any region of the MHC class I locus (chromosome 6p21), or deletion or reducing the expression level of one or more MHC class-I associated genes including, not being limited to, beta-2 microglobulin (B2M) gene, TAP 1 gene, TAP 2 gene and Tapasin genes. For example, the B2M gene encodes a common subunit essential for cell surface expression of all MHC class I heterodimers. B2M null cells are MHC-I deficient. MHC class II deficiency can be achieved by functional deletion or reduction of MHC-II associated genes including, not being limited to, RFXANK, CUT A, RFX5 and RFXAP. CIITA is a transcriptional coactivator, functioning through activation of the transcription factor RFX5 required for class II protein expression. CIITA null cells are MHC-II deficient. In certain embodiments, one or more of the exogenous polynucleotides are integrated at one or more loci of genes selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes to thereby delete or reduce the expression of the gene(s) with the integration.
Other genes for target deletion include, but are not limited to, recombination-activating genes 1 and 2 (RAG1 and RAG2). RAG1 and RAG2 encode parts of a protein complex that initiate V(D)J recombination by introducing double-strand breaks at the border between a recombination signal sequence (RSS) and a coding segment. Deletion or reducing the expression level of the RAG1/RAG2 genes prevents additional TCR rearrangement in the cell, thus preventing unexpected generation of auto-reactive TCR (Minagawa et al., Cell Stem Cell. 2018 Dec 6;23(6):850-858).
In certain embodiments, the exogenous polynucleotides are integrated at one or more loci on the chromosome of the cell, preferably the one or more loci are of genes selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, HI 1, GAPDH, RUNX1, B2M, TAPI, TAP2, Tapasin, NLRC5, CIITA, RFXANK, CIITA, RFX5, RFXAP, TRAC, TRBCl, TRBC2, RAG1, RAG2, NKG2A, NKG2D, CD38, CIS, CBL-B, SOCS2, PD1, CTLA4, LAG3, TIM3, or TIGIT genes, provided at least one of the one or more loci is of a MHC gene, such as a gene selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes. Preferably, the one or more exogenous polynucleotides are integrated at a locus of an MHC class-I associated gene, such as a beta-2 microglobulin (B2M) gene, TAP 1 gene, TAP 2 gene or Tapasin gene; and at a locus of an MHC-II associated gene, such as a RFXANK, CUT A, RFX5, RFXAP, or CIITA gene; and optionally further at a locus of a safe harbor gene selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, Hll, GAPDH, TCR and RUNX1 genes. More preferably, the one or more of the exogenous polynucleotides are integrated at the loci of CIITA, AAVS1 and B2M genes.
In certain embodiments, (i) the exogenous polynucleotide encoding the chimeric antigen receptor (CAR) is integrated at a locus of AAVS1 gene; (ii) the exogenous polypeptide encoding the artificial cell death polypeptide is integrated at a locus of CIITA gene; and (iii) the exogenous polypeptide encoding the human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G) is integrated at a locus of B2M gene; wherein integrations of the exogenous polynucleotides delete or reduce expression of CIITA and B2M genes.
VII. Derivative Cells
In another aspect, the invention relates to a cell derived from differentiation of an iPSC of the application, a derivative cell. As described above, the genomic edits introduced into the iPSC cell are retained in the derivative cell. In certain embodiments of the derivative cell obtained from iPSC differentiation, the derivative cell is a T cell. In other embodiments, the derivative cell is a CD34+ hematopoietic progenitor cell (HPC).
In certain embodiments, the application provides a CD34+ hematopoietic progenitor cell (HPC) derived from an induced pluripotent stem cell (iPSC) comprising: one or more polynucleotides encoding a rearranged ab T cell receptor (TCR), wherein the rearranged ab TCR is restricted for recognition of a non-human peptide in the context of a specific HLA class I (HLA-I) allele, and an exogenous polynucleotide encoding a chimeric antigen receptor (CAR); and one or more of the following additional features: and one or more of the following additional features:
(a) an exogenous polynucleotide encoding an artificial cell death polypeptide;
(b) a deletion or reduced expression of one or more of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes;
(c) a deletion or reduced expression of RAG1 and RAG2 genes; (d) an exogenous polynucleotide encoding a non-naturally occurring variant of FcyRIII (CD 16);
(e) an exogenous polynucleotide encoding interleukin 15 (IL-15) and/or interleukin (EL-15) receptor or a variant or truncation thereof;
(f) an exogeneous polynucleotide encoding a constitutively active interleukin 7 (IL-7) receptor or variant thereof;
(g) an exogenous polynucleotide encoding interleukin 12 (IL-12) or interleukin 21 (IL- 21) or a variant thereof;
(h) an exogenous polynucleotide encoding human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G);
(i) an exogenous polynucleotide encoding leukocyte surface antigen cluster of differentiation CD47 (CD47) and/or CD24; or an exogenous polynucleotide encoding one or more imaging or reporter proteins, such as PSMA or HSV-tk.
In certain embodiments, the application provides a T cell comprising one or more polynucleotides encoding a rearranged ab T cell receptor (TCR), wherein the rearranged ab TCR is restricted for recognition of a non-human peptide in the context of a specific HLA class I (HLA-I) allele, and an exogenous polynucleotide encoding a chimeric antigen receptor (CAR); and one or more of the following additional features:
(a) an exogenous polynucleotide encoding an artificial cell death polypeptide;
(b) a deletion or reduced expression of one or more of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CUT A, RFX5 and RFXAP genes;
(c) a deletion or reduced expression of RAGl and RAG2 genes;
(d) an exogenous polynucleotide encoding a non-naturally occurring variant of FcyRIII (CD 16);
(e) an exogenous polynucleotide encoding interleukin 15 (IL-15) and/or interleukin (IL-15) receptor or a variant or truncation thereof;
(f) an exogeneous polynucleotide encoding a constitutively active interleukin 7 (IL-7) receptor or variant thereof;
(g) an exogenous polynucleotide encoding interleukin 12 (IL-12) or interleukin 21 (IL- 21) or a variant thereof; (h) an exogenous polynucleotide encoding human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G);
(i) an exogenous polynucleotide encoding leukocyte surface antigen cluster of differentiation CD47 (CD47) and/or CD24; or
(j) an exogenous polynucleotide encoding one or more imaging or reporter proteins, such as PSMA or HSV-tk.
In certain embodiments, the rearranged ab TCR enables increased expansion of the differentiated T cell after mitogenic stimulation than a T cell without the rearranged ab TCR.
In certain embodiments, the iPSC is reprogrammed from a ab T cell and the rearranged ab TCR is endogenous to the ab T cell.
In certain embodiments, the ab TCR is recombinant.
In certain embodiments, the iPSC is reprogrammed from peripheral blood mononuclear cells (PBMCs), preferably CD34+ hematopoietic stem cells (HSCs) or ab T cells.
In certain embodiments, the rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
In certain embodiments, the one or more polynucleotides encoding the rearranged ab TCR comprise an a TCR variable gene selected from the group consisting of TRAV27 and TRAV13-1; an a TCRjoining gene selected from the group consisting of TRAJ41 and TRAJ37; and an a TCR constant gene TRAC.
In certain embodiments, the one or more polynucleotides encoding the rearranged ab TCR comprise a b chain variable gene TRBV19; a b chain variable gene selected from the group consisting of TRBJ2-7, TRBJ2-5, and TRBJ2-6; a b chain constant gene selected from the group consisting of TRBCl and TRBC2.
In certain embodiments, the recombinant rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
In certain embodiments, the CD34+ or T cell comprises an exogenous polynucleotide encoding a human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G).
In certain embodiments, one or more of the exogenous polynucleotides are integrated at one or more loci on the chromosome of the cell selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, HI 1, GAPDH, RUNX1, B2M, TAPI, TAP2, Tapasin, NLRC5, CIITA, RFXANK, CIITA, RFX5, RFXAP, TRAC, TRBCl, TRBC2, RAG1, RAG2, NKG2A, NKG2D, CD38, CIS, CBL-B, SOCS2, PD1, CTLA4, LAG3, TIM3, or TIGIT genes, provided at least one of the exogenous polynucleotides is integrated at a locus of a gene selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes to thereby result in a deletion or reduced expression of the gene. In certain embodiments, one or more of the exogenous polynucleotides are integrated at the loci of the CIITA, AAVS1 and B2M genes.
In certain embodiments, the exogenous polynucleotide encoding the chimeric antigen receptor (CAR) is integrated at a locus of AAVS1 gene; the exogenous polypeptide encoding the artificial cell death polypeptide is integrated at a locus of CIITA gene; and the exogenous polypeptide encoding the human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G) is integrated at a locus of B2M gene; wherein integration of the exogenous polynucleotides deletes or reduces expression of CIITA and B2M.
Also provided is a T cell comprising: (i) an exogenous polynucleotide encoding a chimeric antigen receptor (CAR) having the amino acid sequence of SEQ ID NO: 61; (ii) an exogenous polynucleotide encoding an artificial cell death polypeptide comprising an apoptosis- inducing domain having the amino acid sequence of SEQ ID NO: 71; (iii) a polynucleotide encoding a rearranged T cell receptor (TCR) locus comprising a a TCR having the amino acid sequence of SEQ ID NO: 86, and a b TCR having the amino acid sequence of SEQ ID NO: 87; and (iv) optionally, an exogenous polynucleotide encoding a human leukocyte antigen E (HLA- E) having the amino acid sequence of SEQ ID NO: 66; wherein one or more of the exogenous polynucleotides are integrated at loci of AAVS1, CIITA and B2M genes, to thereby delete or reduce expression of CIITA and B2M.
VIII. Methods of Differentiation
Also provided is a method of manufacturing the T cell of the application, comprising differentiating an iPSC cell of the application under conditions for cell differentiation to thereby obtain the T cell.
An iPSC of the application can be differentiated by any method known in the art. Exemplary methods are described in US8372642, US8574179, US10100282, US10865381, , W02010/099539, W02012/109208, WO2017/070333, W02017/070337, WO2018/067836, WO2018/195175, W02020/061256, WO2017/179720, W02016/010148, and WO2018/048828, each of which are herein incorporated by reference in its entirety. The differentiation protocol can use feeder cells or can be feeder-free. As used herein, “feeder cells” or “feeders” are terms describing cells of one type that are co-cultured with cells of a second type to provide an environment in which the cells of the second type can grow, expand, or differentiate, as the feeder cells provide stimulation, growth factors and nutrients for the support of the second cell type.
Notch signaling, in particular, plays a key role in driving precursor cells towards a T cell fate. In the human thymus, the Notch family proteins DLL1, DLL4, and Jag2 (expressed by stromal cells in the thymus) signal through the receptor Notchl (expressed by early thymocytes).
In a general aspect, the application also provides a method of differentiating CD34+ hematopoietic progenitor cell (HPC) comprising a polynucleotide encoding a rearranged TCR, such as an induced-pluripotent stem cell (iPSC)-derived CD34+ HPC comprising a polynucleotide encoding a rearranged TCR, to a T cell, the method comprising culturing the CD34+ HPC in a medium comprising Delta-like protein 4 (DLL4) and Jagged 2 (JAG2), optionally further comprising a fibronectin protein or fragment thereof, SCF, FLT3L, TPO, and/or IL-7. In certain embodiments, the DLL4 and JAG2 proteins are immobilized on a cell culture plate, for example, using poly dopamine in the presence or absence of Protein G coating. In certain embodiments, the cells are cultured in the medium comprising DLL4 and JAG2 for about 21 to about 35 days, such as 21 days, 28 35 days, or any number of days in between.
In certain embodiments, the recombinant DLL4 is a variant DLL4. Non-limiting exemplary DLL4 variants and sequences are provided in Table 2.
Table 2.
Figure imgf000066_0001
Extracellular Domain (ECD); Epidermal growth factor (EGF) repeat; N = amino terminus In certain embodiments, the method further comprises culturing the cells in a medium comprising one or more cytokines selected from the group consisting of interleukin-2 (IL-2), IL- 7, and EL-15. In certain embodiments, the cells are cultured with the cytokine for 1 to 35 days. In particular embodiments, the method comprises culturing the cells in medium comprising IL-2, IL-7 and IL-15. In a particular embodiment, the IL-2, IL-7 and IL-15 are added to the medium on day 21 of differentiation.
In certain embodiments, the method further comprises culturing the cells in medium comprising an anti-CD3 antibody. In certain embodiments, the anti-CD3 antibody is immobilized on a cell culture plate, for example, direct absorption onto plastic materials such as polystyrene. Non-limiting examples of anti-CD3 antibodies are OKT3 and UCHT1 as described in as described in Rung et al, Science. 1979 Oct 19;206(4416):347-9 and Callard et ak, Clin Exp Immunol. 1981 Mar;43(3):497-505, respectively, the disclosures of which are herein incorporated by reference. In certain embodiments, the anti-CD3 antibody is OKT3. In certain embodiments, the anti-CD3 antibody is UCHT1.
Also provided is a method of differentiating an induced-pluripotent stem cell (iPSC)- derived CD34+ hematopoietic progenitor cell (HPC) comprising a rearranged TCR to a T cell, the method comprising:
(a) culturing the cell in medium comprising Delta-like protein 4 (DLL4) and recombinant Jagged 2 (JAG2), optionally further comprising a fibronectin protein or fragment thereof optionally further comprising a fibronectin protein or fragment thereof, SCF, FLT3L, TPO, and/or IL-7;
(b) culturing the cell in medium comprising interleukin-2 (IL-2), IL-7, and IL-15; and
(c) culturing the cell in medium comprising an anti-CD3 antibody, preferably OKT3 or UCHT1.
In certain embodiments, the cell is cultured in the medium comprising DLL4 and JAG2 for about 21 to about 35 days, such as 21 days, 28 days, 35 days, or any number of days in between.
In certain embodiments, the cell is cultured in the medium comprising DLL4 and JAG2 from day 0 to about day 21 of differentiation.
In certain embodiments, the cell is cultured in medium comprising IL-2, IL-7, and IL-15 from day 21 to about day 28 of differentiation. In certain embodiments, the cell is cultured in medium comprising an anti-CD3 antibody, such as OKT3 or UCHT1, day 21 to about day 28 of differentiation.
In certain embodiments, the cell is cultured in medium comprising IL-2, IL-7, and IL-15, and an anti-CD3 antibody, such as OKT3 or UCHT1, from day 21 to about day 28 of differentiation.
IX. Polynucleotides, vectors, and host cells (1) Nucleic acids encoding a CAR
In another general aspect, the invention relates to an isolated nucleic acid encoding a chimeric antigen receptor (CAR) useful for an invention according to embodiments of the application. It will be appreciated by those skilled in the art that the coding sequence of a CAR can be changed (e.g., replaced, deleted, inserted, etc.) without changing the amino acid sequence of the protein. Accordingly, it will be understood by those skilled in the art that nucleic acid sequences encoding CARs of the application can be altered without changing the amino acid sequences of the proteins.
In certain embodiments, the isolated nucleic acid encodes a CAR targeting CD 19. In a particular embodiment, the isolated nucleic acid encoding the CAR comprises a polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 62, preferably the polynucleotide sequence of SEQ ID NO: 62.
In another general aspect, the application provides a vector comprising a polynucleotide sequence encoding a CAR useful for an invention according to embodiments of the application. Any vector known to those skilled in the art in view of the present disclosure can be used, such as a plasmid, a cosmid, a phage vector or a viral vector. In some embodiments, the vector is a recombinant expression vector such as a plasmid. The vector can include any element to establish a conventional function of an expression vector, for example, a promoter, ribosome binding element, terminator, enhancer, selection marker, and origin of replication. The promoter can be a constitutive, inducible, or repressible promoter. A number of expression vectors capable of delivering nucleic acids to a cell are known in the art and can be used herein for production of a CAR in the cell. Conventional cloning techniques or artificial gene synthesis can be used to generate a recombinant expression vector according to embodiments of the application.
In a particular aspect, the application provides vectors for targeted integration of a CAR useful for an invention according to embodiments of the application. In certain embodiments, the vector comprises an exogenous polynucleotide having, in the 5’ to 3’ order, (a) a promoter; (b) a polynucleotide sequence encoding a CAR according to an embodiment of the application; and (c) a terminator/polyadenylation signal.
In certain embodiments, the promoter is a CAG promoter. In certain embodiments, the CAG promoter comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 63. Other promoters can also be used, examples of which include, but are not limited to, EFla, UBC, CMV, SV40, PGK1, and human beta actin.
In certain embodiments, the terminator/ polyadenylation signal is a SV40 signal. In certain embodiments, the SV40 signal comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 64. Other terminator sequences can also be used, examples of which include, but are not limited to, BGH, hGH, and PGK.
In certain embodiments, the polynucleotide sequence encoding a CAR comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 62.
In some embodiment, the vector further comprises a left homology arm and a right homology arm flanking the exogenous polynucleotide. As used herein, “left homology arm” and “right homology arm” refers to a pair of nucleic acid sequences that flank an exogenous polynucleotide and facilitate the integration of the exogenous polynucleotide into a specified chromosomal locus. Sequences of the left and right arm homology arms can be designed based on the integration site of interest. In some embodiment, the left or right arm homology arm is homologous to the left or right side sequence of the integration site.
In certain embodiments, the left homology arm comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 80. In certain embodiments, the right homology arm comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 81.
In a particular embodiment, the vector comprises a polynucleotide sequence at least 85%, such as at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 82, preferably the polynucleotide sequence of SEQ ID NO:
82.
(2) Nucleic acids encoding an inactivated cell surface receptor
In another general aspect, the invention relates to an isolated nucleic acid encoding an inactivated cell surface receptor useful for an invention according to embodiments of the application. It will be appreciated by those skilled in the art that the coding sequence of an inactivated cell surface receptor can be changed (e.g., replaced, deleted, inserted, etc.) without changing the amino acid sequence of the protein. Accordingly, it will be understood by those skilled in the art that nucleic acid sequences encoding an inactivated cell surface receptor of the application can be altered without changing the amino acid sequences of the proteins.
In certain embodiments, an isolated nucleic acid encodes any inactivated cell surface receptor described herein, such as that comprises a monoclonal antibody-specific epitope, and a cytokine, wherein the monoclonal antibody-specific epitope and the cytokine are operably linked by an autoprotease peptide sequence.
In some embodiments, the isolated nucleic acid encodes an inactivated cell surface receptor comprising an epitope specifically recognized by an antibody, such as ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, polatuzumab vedotin, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimumab, belimumab, canakinumab, denosumab, golimumab, ipilimumab, ofatumumab, panitumumab, or ustekinumab.
In certain embodiments, the isolated nucleic acid encodes an inactivated cell surface receptor having a truncated epithelial growth factor (tEGFR) variant. Preferably, the inactivated cell surface receptor comprises an epitope specifically recognized by cetuximab, matuzumab, necitumumab or panitumumab, preferably cetuximab.
In certain embodiments, the isolated nucleic acid encodes an inactivated cell surface receptor having one or more epitopes of CD79b, such as an epitope specifically recognized by polatuzumab vedotin. In certain embodiments, the isolated nucleic acid encodes an inactivated cell surface receptor having one or more epitopes of CD20, such as an epitope specifically recognized by rituximab.
In certain embodiments, the isolated nucleic acid encodes an inactivated cell surface receptor having one or more epitopes of Her 2 receptor, such as an epitope specifically recognized by trastuzumab
In certain embodiments, the autoprotease peptide sequence is porcine tesehovirus-1 2A
(P2A).
In certain embodiments, the truncated epithelial growth factor (tEGFR) variant consists of an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 71.
In certain embodiments, the monoclonal antibody-specific epitope specifically recognized by polatuzumab vedotin consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 74.
In certain embodiments, the monoclonal antibody-specific epitope specifically recognized by rituximab consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 75.
Inc certain embodiments, the monoclonal antibody-specific epitope specifically recognized by trastuzumab consists of an amino acid sequence at least 90%, such as at least 90%, 91%, 82%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%, identical to SEQ ID NO: 76.
In certain embodiments, the autoprotease peptide has an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 72.
In another general aspect, the application provides a vector comprising a polynucleotide sequence encoding an inactivated cell surface receptor useful for an invention according to embodiments of the application. Any vector known to those skilled in the art in view of the present disclosure can be used, such as a plasmid, a cosmid, a phage vector or a viral vector. In some embodiments, the vector is a recombinant expression vector such as a plasmid. The vector can include any element to establish a conventional function of an expression vector, for example, a promoter, ribosome binding element, terminator, enhancer, selection marker, and origin of replication. The promoter can be a constitutive, inducible, or repressible promoter. A number of expression vectors capable of delivering nucleic acids to a cell are known in the art and can be used herein for production of an inactivated cell surface receptor in the cell. Conventional cloning techniques or artificial gene synthesis can be used to generate a recombinant expression vector according to embodiments of the application.
In a particular aspect, the application provides a vector for targeted integration of an inactivated cell surface receptor useful for an invention according to embodiments of the application. In certain embodiments, the vector comprises an exogenous polynucleotide having, in the 5’ to 3’ order, (a) a promoter; (b) a polynucleotide sequence encoding an inactivated cell surface receptor, such as an inactivated cell surface receptor comprising a truncated epithelial growth factor (tEGFR) variant.
In certain embodiments, the promoter is a CAG promoter. In certain embodiments, the CAG promoter comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 63. Other promoters can also be used, examples of which include, but are not limited to, EFla, UBC, CMV, SV40, PGK1, and human beta actin.
In certain embodiments, the terminator/polyadenylation signal is a SV40 signal. In certain embodiments, the SV40 signal comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 64. Other terminator sequences can also be used, examples of which include, but are not limited to BGH, hGH, and PGK.
In some embodiment, the vector further comprises a left homology arm and a right homology arm flanking the exogenous polynucleotide.
(3) Nucleic acids encoding an HLA construct
In another general aspect, the invention relates to an isolated nucleic acid encoding an HLA construct useful for an invention according to embodiments of the application. It will be appreciated by those skilled in the art that the coding sequence of an HLA construct can be changed (e.g., replaced, deleted, inserted, etc.) without changing the amino acid sequence of the protein. Accordingly, it will be understood by those skilled in the art that nucleic acid sequences encoding an HL A construct of the application can be altered without changing the amino acid sequences of the proteins. In certain embodiments, the isolated nucleic acid encodes an HLA construct comprising a signal peptide, such as an HLA-G signal peptide, operably linked to an HLA coding sequence, such as a coding sequence of a mature B2M, and/or a mature HLA-E. In some embodiments, the HLA coding sequence encodes the HLA-G and B2M, which are operably linked by a 4X GGGGS linker, and/or the B2M and HLA-E, which are operably linked by a 3X GGGGS linker. In a particular embodiment, the isolated nucleic acid encoding the HLA construct comprises a polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 67, preferably the polynucleotide sequence of SEQ ID NO: 67. In another embodiment, the isolated nucleic acid encoding the HLA construct comprises a polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 70, preferably the polynucleotide sequence of SEQ ID NO: 70.
In another general aspect, the application provides a vector comprising a polynucleotide sequence encoding a HLA construct useful for an invention according to embodiments of the application. Any vector known to those skilled in the art in view of the present disclosure can be used, such as a plasmid, a cosmid, a phage vector or a viral vector. In some embodiments, the vector is a recombinant expression vector such as a plasmid. The vector can include any element to establish a conventional function of an expression vector, for example, a promoter, ribosome binding element, terminator, enhancer, selection marker, and origin of replication. The promoter can be a constitutive, inducible, or repressible promoter. A number of expression vectors capable of delivering nucleic acids to a cell are known in the art and can be used herein for production of a HLA construct in the cell. Conventional cloning techniques or artificial gene synthesis can be used to generate a recombinant expression vector according to embodiments of the application.
In a particular aspect, the application provides vectors for targeted integration of a HLA construct useful for an invention according to embodiments of the application. In certain embodiments, the vector comprises an exogenous polynucleotide having, in the 5’ to 3’ order, (a) a promoter; (b) a polynucleotide sequence encoding an HLA construct; and (c) a terminator/polyadenylation signal.
In certain embodiments, the promoter is a CAG promoter. In certain embodiments, the CAG promoter comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 63. Other promoters can also be used, examples of which include, but are not limited to, EFla, UBC, CMV, SV40, PGK1, and human beta actin.
In certain embodiments, the terminator/ polyadenylation signal is a SV40 signal. In certain embodiments, the SV40 signal comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 64. Other terminator sequences can also be used, examples of which include, but are not limited to BGH, hGH, and PGK
In certain embodiments, a polynucleotide sequence encoding a HLA construct comprises a signal peptide, such as a HLA-G signal peptide, a mature B2M, and a mature HLA-E, wherein the HLA-G and B2M are operably linked by a 4X GGGGS linker (SEQ ID NO: 31) and the B2M transgene and HLA-E are operably linked by a 3X GGGGS linker (SEQ ID NO: 25). In particular embodiments, the HLA construct comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 67, preferably the polynucleotide sequence of SEQ ID NO: 67. In another embodiment, the HLA construct comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 70, preferably the polynucleotide sequence of SEQ ID NO: 70.
In some embodiment, the vector further comprises a left homology arm and a right homology arm flanking the exogenous polynucleotide.
In certain embodiments, the left homology arm comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 77. In certain embodiments, the right homology arm comprises the polynucleotide sequence at least 90%, such as at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 78.
In a particular embodiment, the vector comprises a polynucleotide sequence at least 85%, such as at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 100%, identical to SEQ ID NO: 79, preferably the polynucleotide sequence of SEQ ID NO: 79.
(4) Host cells
In another general aspect, the application provides a host cell comprising a vector of the application and/or an isolated nucleic acid encoding a construct of the application. Any host cell known to those skilled in the art in view of the present disclosure can be used for recombinant expression of exogenous polynucleotides of the application. According to particular embodiments, the recombinant expression vector is transformed into host cells by conventional methods such as chemical transfection, heat shock, or electroporation, where it is stably integrated into the host cell genome such that the recombinant nucleic acid is effectively expressed.
Examples of host cells include, for example, recombinant cells containing a vector or isolated nucleic acid of the application useful for the production of a vector or construct of interest; or an engineered iPSC or derivative cell thereof containing one or more isolated nucleic acids of the application, preferably integrated at one or more chromosomal loci. A host cell of an isolated nucleic acid of the application can also be an immune effector cell, such as a T cell, comprising the one or more isolated nucleic acids of the application. The immune effector cell can be obtained by differentiation of an engineered iPSC of the application. Any suitable method in the art can be used for the differentiation in view of the present disclosure. The immune effector cell can also be obtained transfecting an immune effector cell with one or more isolated nucleic acids of the application.
IX. Compositions
In another general aspect, the application provides a composition comprising an isolated polynucleotide of the application, a host cell and/or an iPSC or derivative cell thereof of the application.
In certain embodiments, the composition further comprises one or more therapeutic agents selected from the group consisting of a peptide, a cytokine, a checkpoint inhibitor, a mitogen, a growth factor, a small RNA, a dsRNA (double stranded RNA), siRNA, oligonucleotide, mononuclear blood cells, , a vector comprising one or more polynucleic acids of interest, an antibody, a chemotherapeutic agent or a radioactive moiety, or an immunomodulatory drug (IMiD).
In certain embodiments, the composition is a pharmaceutical composition comprising an isolated polynucleotide of the application, a host cell and/or an iPSC or derivative cell thereof of the application and a pharmaceutically acceptable carrier. The term “pharmaceutical composition” as used herein means a product comprising an isolated polynucleotide of the application, an isolated polypeptide of the application, a host cell of the application, and/or an iPSC or derivative cell thereof of the application together with a pharmaceutically acceptable carrier. Polynucleotides, polypeptides, host cells, and/or iPSCs or derivative cells thereof of the application and compositions comprising them are also useful in the manufacture of a medicament for therapeutic applications mentioned herein.
As used herein, the term “carrier” refers to any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containing vesicle, microsphere, liposomal encapsulation, or other material well known in the art for use in pharmaceutical formulations. It will be understood that the characteristics of the carrier, excipient or diluent will depend on the route of administration for a particular application. As used herein, the term “pharmaceutically acceptable carrier” refers to a non-toxic material that does not interfere with the effectiveness of a composition described herein or the biological activity of a composition described herein. According to particular embodiments, in view of the present disclosure, any pharmaceutically acceptable carrier suitable for use in a polynucleotide, polypeptide, host cell, and/or iPSC or derivative cell thereof can be used.
The formulation of pharmaceutically active ingredients with pharmaceutically acceptable carriers is known in the art, e.g., Remington: The Science and Practice of Pharmacy (e.g.
21st edition (2005), and any later editions). Non-limiting examples of additional ingredients include: buffers, diluents, solvents, tonicity regulating agents, preservatives, stabilizers, and chelating agents. One or more pharmaceutically acceptable carrier can be used in formulating the pharmaceutical compositions of the application.
X. Methods of use
In another general aspect, the application provides a method of treating a disease or a condition in a subject in need thereof. The methods comprise administering to the subject in need thereof a therapeutically effective amount of cells of the application and/or a composition of the application. In certain embodiments, the disease or condition is cancer. The cancer can, for example, be a solid or a liquid cancer. The cancer, can, for example, be selected from the group consisting of a lung cancer, a gastric cancer, a colon cancer, a liver cancer, a renal cell carcinoma, a bladder urothelial carcinoma, a metastatic melanoma, a breast cancer, an ovarian cancer, a cervical cancer, a head and neck cancer, a pancreatic cancer, an endometrial cancer, a prostate cancer, a thyroid cancer, a glioma, a glioblastoma, and other solid tumors, and a non- Hodgkin’ s lymphoma (NHL), Hodgkin’s lymphoma/disease (HD), an acute lymphocytic leukemia (ALL), a chronic lymphocytic leukemia (CLL), a chronic myelogenous leukemia (CML), a multiple myeloma (MM), an acute myeloid leukemia (AML), and other liquid tumors. In a preferred embodiment, the cancer is a non-Hodgkin’s lymphoma (NHL).
According to embodiments of the application, the composition comprises a therapeutically effective amount of an isolated polynucleotide, an isolated polypeptide, a host cell, and/or an iPSC or derivative cell thereof. As used herein, the term “therapeutically effective amount” refers to an amount of an active ingredient or component that elicits the desired biological or medicinal response in a subject. A therapeutically effective amount can be determined empirically and in a routine manner, in relation to the stated purpose.
As used herein with reference to a cell of the application and/or a pharmaceutical composition of the application a therapeutically effective amount means an amount of the cells and/or the pharmaceutical composition that modulates an immune response in a subject in need thereof.
According to particular embodiments, a therapeutically effective amount refers to the amount of therapy which is sufficient to achieve one, two, three, four, or more of the following effects: (i) reduce or ameliorate the severity of the disease, disorder or condition to be treated or a symptom associated therewith; (ii) reduce the duration of the disease, disorder or condition to be treated, or a symptom associated therewith; (iii) prevent the progression of the disease, disorder or condition to be treated, or a symptom associated therewith; (iv) cause regression of the disease, disorder or condition to be treated, or a symptom associated therewith; (v) prevent the development or onset of the disease, disorder or condition to be treated, or a symptom associated therewith; (vi) prevent the recurrence of the disease, disorder or condition to be treated, or a symptom associated therewith; (vii) reduce hospitalization of a subject having the disease, disorder or condition to be treated, or a symptom associated therewith; (viii) reduce hospitalization length of a subject having the disease, disorder or condition to be treated, or a symptom associated therewith; (ix) increase the survival of a subject with the disease, disorder or condition to be treated, or a symptom associated therewith; (xi) inhibit or reduce the disease, disorder or condition to be treated, or a symptom associated therewith in a subject; and/or (xii) enhance or improve the prophylactic or therapeutic effect(s) of another therapy.
In particular embodiments, the cells of the invention are allogeneic to the patient being treated. The therapeutically effective amount or dosage can vary according to various factors, such as the disease, disorder or condition to be treated, the means of administration, the target site, the physiological state of the subject (including, e.g., age, body weight, health), whether the subject is a human or an animal, other medications administered, and whether the treatment is prophylactic or therapeutic. Treatment dosages are optimally titrated to optimize safety and efficacy.
According to particular embodiments, the compositions described herein are formulated to be suitable for the intended route of administration to a subject. For example, the compositions described herein can be formulated to be suitable for intravenous, subcutaneous, or intramuscular administration.
The cells of the application and/or the pharmaceutical compositions of the application can be administered in any convenient manner known to those skilled in the art. For example, the cells of the application can be administered to the subject by aerosol inhalation, injection, ingestion, transfusion, implantation, and/or transplantation. The compositions comprising the cells of the application can be administered transarterially, subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, inrapleurally, by intravenous (i.v.) injection, or intraperitoneally. In certain embodiments, the cells of the application can be administered with or without lymphodepletion of the subject.
The pharmaceutical compositions comprising cells of the application can be provided in sterile liquid preparations, typically isotonic aqueous solutions with cell suspensions, or optionally as emulsions, dispersions, or the like, which are typically buffered to a selected pH. The compositions can comprise carriers, for example, water, saline, phosphate buffered saline, and the like, suitable for the integrity and viability of the cells, and for administration of a cell composition. Sterile injectable solutions can be prepared by incorporating cells of the application in a suitable amount of the appropriate solvent with various other ingredients, as desired. Such compositions can include a pharmaceutically acceptable carrier, diluent, or excipient such as sterile water, physiological saline, glucose, dextrose, or the like, that are suitable for use with a cell composition and for administration to a subject, such as a human. Suitable buffers for providing a cell composition are well known in the art. Any vehicle, diluent, or additive used is compatible with preserving the integrity and viability of the cells of the application. The cells of the application and/or the pharmaceutical compositions of the application can be administered in any physiologically acceptable vehicle. A cell population comprising cells of the application can comprise a purified population of cells. Those skilled in the art can readily determine the cells in a cell population using various well known methods. The ranges in purity in cell populations comprising genetically modified cells of the application can be from about 50% to about 55%, from about 55% to about 60%, from about 60% to about 65%, from about 65% to about 70%, from about 70% to about 75%, from about 75% to about 80%, from about 80% to about 85%, from about 85% to about 90%, from about 90% to about 95%, or from about 95% to about 100%. Dosages can be readily adjusted by those skilled in the art, for example, a decrease in purity could require an increase in dosage.
The cells of the application are generally administered as a dose based on cells per kilogram (cells/kg) of body weight of the subject to which the cells and/or pharmaceutical compositions comprising the cells are administered. Generally, the cell doses are in the range of about 104 to about 1010 cells/kg of body weight, for example, about 105 to about 109, about 105 to about 108, about 105 to about 107, or about 105 to about 106, depending on the mode and location of administration. In general, in the case of systemic administration, a higher dose is used than in regional administration, where the immune cells of the application are administered in the region of a tumor and/or cancer. Exemplary dose ranges include, but are not limited to, 1 x 104 to 1 x 108, 2 x 104 to 1 x 108, 3 x 104 to 1 x 108, 4 x 104 to 1 x 108, 5 x 104 to 6 x 108, 7 x 104 to 1 x 108, 8 x 104 to 1 x 10s, 9 x 104 to 1 x 108, 1 x 105 to 1 x 108, 1 x 105 to 9 x 107, 1 x 105 to 8 x 107, 1 x 105 to 7 x 107, 1 x 105 to 6 x 107, 1 x 105 to 5 x 107, 1 x 103 to 4 x 107, 1 x 105 to 4 x 107,
1 x 105 to 3 x 107, 1 x 105 to 2 x 107, 1 x 105 to 1 x 107, 1 x 105 to 9 x 106, 1 x 105 to 8 x 106, 1 x 105 to 7 x 106, 1 x 105 to 6 x 106, 1 x 105 to 5 x 106, 1 x 105 to 4 x 106, 1 x 105 to 4 x 106, 1 x 105 to 3 x 106, 1 x 105 to 2 x 106, 1 x 105 to 1 x 106, 2 x 105 to 9 x 107, 2 x 105 to 8 x 107, 2 x 105 to 7 x 10', 2 x 105 to 6 x 107, 2 x 105 to 5 x 107, 2 x 105 to 4 x 107, 2 x 105 to 4 x 107, 2 x 105 to 3 x 107, 2 x 105 to 2 x 107, 2 x 105 to 1 x 107, 2 x 105 to 9 x 106, 2 x 105 to 8 x 106, 2 x 105 to 7 x 106,
2 x 105 to 6 x 106, 2 x 105 to 5 x 106, 2 x 105 to 4 x 106, 2 x 105 to 4 x 106, 2 x 105 to 3 x 106, 2 x 105 to 2 x 106, 2 x 105 to l x 106, 3 x 105 to 3 x 106 cells/kg, and the like. Additionally, the dose can be adjusted to account for whether a single dose is being administered or whether multiple doses are being administered. The precise determination of what would be considered an effective dose can be based on factors individual to each subject. As used herein, the terms “treat,” “treating,” and “treatment” are all intended to refer to an amelioration or reversal of at least one measurable physical parameter related to a cancer, which is not necessarily discernible in the subject, but can be discernible in the subject. The terms “treat,” “treating,” and “treatment,” can also refer to causing regression, preventing the progression, or at least slowing down the progression of the disease, disorder, or condition. In a particular embodiment, “treat,” “treating,” and “treatment” refer to an alleviation, prevention of the development or onset, or reduction in the duration of one or more symptoms associated with the disease, disorder, or condition, such as a tumor or more preferably a cancer. In a particular embodiment, “treat,” “treating,” and “treatment” refer to prevention of the recurrence of the disease, disorder, or condition. In a particular embodiment, “treat,” “treating,” and “treatment” refer to an increase in the survival of a subject having the disease, disorder, or condition. In a particular embodiment, “treat,” “treating,” and “treatment” refer to elimination of the disease, disorder, or condition in the subject.
The cells of the application and/or the pharmaceutical compositions of the application can be administered in combination with one or more additional therapeutic agents. In certain embodiments the one or more therapeutic agents are selected from the group consisting of a peptide, a cytokine, a checkpoint inhibitor, a mitogen, a growth factor, a small RNA, a dsRNA (double stranded RNA), siRNA, oligonucleotide, mononuclear blood cells, a vector comprising one or more polynucleic acids of interest, an antibody, a chemotherapeutic agent or a radioactive moiety, or an immunomodulatory drug (IMiD). Examples of useful secondary or adjunctive therapeutic agents that can be used with the cells of the invention include, but are not limited to: chemotherapeutic agents including alkylating agents such as thiotepa and cyclophaophamide, alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, corboquone; ethyleneimines and methylamelamines including altreamine, triethylenemelamine, trietyelenephosphoramide; delta-9-tetrahydocannabinol; a camptothecin, irinotecan , acetylcamptothecin, scopolectin, and 9-aminocamptothecin); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); podophyllotoxin; podophyllinic acid; teniposide; cryptophycms (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB 1-T ); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlomaphazine, cholophosphamide, estramustine, ifosfamde, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustme; antibiotics such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gammall and calicheamicin omegall (see, e.g, Agnew, Chem. Inti. Ed. Engl., 33: 183-186 (1994)); dynemicin, including dynemicin A; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzmophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including ADRIAMYCIN®, morpholino-doxorubicin, cyanomorpholinodoxorubicin, 2-pyrrolino-doxorubicin, doxorubicin HC1 liposome injection (DOXIL®) and deoxy doxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti -metabolites such as methotrexate, gemcitabine (GEMZAR®), tegafur (UFTORAL®), capecitabine (XELODA®), an epothilone, and 5- fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabme, 6-mercaptopurme, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridme, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elformithine; elliptinium acetate; etoglucid; gallium nitrate; hydroxyurea; lentinan; lomdainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; 2-ethylhydrazide; procarbazine; PSK® polysaccharide complex (JHS Natural Products, Eugene, Oreg.); razoxane; rhizoxin; sizofuran; spirogermamum; tenuazonic acid; triaziquone; 2,2',2"-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine (ELDISINE®, FILDESIN®); dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside ("Ara-C"); thiotepa; taxoids, e.g, paclitaxel (TAXOL®), albuminengineered nanoparticle formulation of paclitaxel (ABRAXANET™), and doxetaxel (TAXOTERE®); chloranbucil; 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine (VELBAN®); platinum; etoposide (VP- 16); ifosfamide; mitoxantrone; vincristine (ONCOVIN®); oxaliplatin; leucovovin; vinorelbine (NAVELBINE®); novantrone; edatrexate; daunomycm; aminopterm; cyclosporine, sirolimus, rapamycin, rapalogs, ibandronate; topoisomerase inhibitor RFS 2000; difluoromethylomithine (DMFO); retinoids such as retinoic acid; CHOP, an abbreviation for a combined therapy of cyclophosphamide, doxorubicin, vincristine, and prednisolone, and FOLFOX, an abbreviation for a treatment regimen with oxahplatin (ELOXATIN™) combined with 5-FU, leucovovm; anti-estrogens and selective estrogen receptor modulators (SERMs), including, for example, tamoxifen (including NOLVADEX® tamoxifen), raloxifene (EVISTA®), droloxifene, 4-hydroxytamoxifen, trioxifene, keoxifene, LY1 17018, onapristone, and toremifene (FARESTON®); anti-progesterones; estrogen receptor down-regulators (ERDs); estrogen receptor antagonists such as fulvestrant (FASLODEX®); agents that function to suppress or shut down the ovaries, for example, leutinizing hormone-releasing hormone (LHRH) agonists such as leuprohde acetate (LUPRON® and ELIGARD®), goserelin acetate, buserelin acetate and tripterelin; other antiandrogens such as flutamide, nilutamide and bicalutamide; and aromatase inhibitors that inhibit the enzyme aromatase, which regulates estrogen production in the adrenal glands, such as, for example, 4(5)-imidazoles, aminoglutethimide, megestrol acetate (MEGASE®), exemestane (AROMASIN®), formestanie, fadrozole, vorozole (RIVISOR®), letrozole (FEMARA®), and anastrozole (ARIMIDEX®); bisphosphonates such as clodronate (for example, BONEFOS® or OST AC®), etidronate (DIDROCAL®), NE-58095, zoledronic acid/zoledronate (ZOMETA®), alendronate (FOSAMAX®), pamidronate (AREDIA®), tiludronate (SKELID®), or risedronate (ACTONEL®); troxacitabine (a 1,3-dioxolane nucleoside cytosine analog); aptamers, described for example in U.S. Pat. No. 6,344,321, which is herein incorporated by reference in its entirety; anti HGF monoclonal antibodies (e.g., AV299 from Aveo, AMG102, from Amgen); truncated mTOR variants (e.g., CGEN241 from Compugen); protein kinase inhibitors that block mTOR induced pathways (e.g.,ARQ197 from Arqule, XL880 from Exelexis, SGX523 from SGX Pharmaceuticals, MP470 from Supergen, PF2341066 from Pfizer); vaccines such as THERATOPE® vaccine and gene therapy vaccines, for example, ALLOVECTIN® vaccine, LEUVECTIN® vaccine, and VAXID® vaccine; topoisomerase 1 inhibitor (e.g., LURTOTECAN®); rmRH (e.g., ABARELIX®); lapatinib ditosylate (an ErbB-2 and EGFR dual tyrosine kinase small molecule inhibitor also known as GW572016); COX-2 inhibitors such as celecoxib (CELEBREX®; 4-(5-( 4-methylphenyl)-3-(trifluoromethyl)-lH-pyrazol-l-yl) benzenesulfonamide; and pharmaceutically acceptable salts, acids or derivatives of any of the above. EXAMPLES
Example 1. Generating ab iT cell
Three methods can be used for creating the iPSCs that are used to make ab CAR-iT cells. One route uses ab T cells that are collected from blood of donors. These T cells possess rearranged a and b gene clusters, so when they are reprogrammed to become iPSCs, the resulting TiPSCs (T cell-derived iPSCs) possess the same genetic rearrangements. The ab TCRs have known antigen specificity and HLA-restriction (FIG. 1A). Another method begins with a non-T cell from a donor. The cell type can be any somatic cell, preferably cells used for this process are peripheral blood hematopoietic stem cells (HSCs) that are defined by expression of the surface protein CD34. These PiPSC (peripheral blood CD34 HSC-derived iPSCs), can be converted into a T-PiPSC (TCR-expressing PiPSC) via genetic engineering to knock-in a set of trusted rearranged ab TCR transgenes (FIG. IB). A third method uses ab T cells that are collected from blood of donors. The ab T cells can be converted into a T-iPSC (TCR-expressing iPSC) via genetic engineering to replace the endogenous ab TCR locus with trusted rearranged ab TCR transgenes (FIG. 1C). The rearranged TCR transgenes for a and b chains are delivered as a single polycistronic construct or as two separate constructs: one alpha and one beta.
Generating PiPSC
First, peripheral blood mononuclear cells (PBMCs) were collected from healthy donors. Then, hematopoietic stem cells (HSCs) were isolated that are defined by expression of the surface protein CD34.
The proliferating HSCs are subjected to iPSC reprogramming. The iPSCs were reprogrammed using methods known in the art. Exemplary methods of iPSC reprogramming are described in U.S. Pat. Nos. 8,183,038; 8,268,620; 8,440,461; 9,499,786; 10,865,381; 8,952,801; 8,546,140; 9,644,184; 9,328,332; and 8,765,470, each of which is incorporated by reference in its entirety.
Generating TiPSC
There are two strategies for generating TiPSC. One approach does not require knowledge of the HLA type of the donor or antigen specificity of the TCR. Any ab T cell can be reprogrammed into a TiPSC and the unknown TCR replaced with a known trusted TCR through genetic engineering (FIG. 1C). In order to reprogram ab T cells, PBMCs are collected from a donor and cultured in the presence of stimuli that cause mitosis of T cells. These can include antibodies that act as agonists for the CD3 molecule and CD28 molecule, non-specific mitogens such as phytohemmaglutinin (PHA), or other T cell mitogens. When employed in the presence of IL-2, mitogens cause T cell proliferation and render the T cells susceptible to iPSC reprogramming using methods known in the art. Exemplary methods of iPSC reprogramming are described in U.S. Pat. Nos. 8,183,038; 8,268,620; 8,440,461; 9,499,786; 10,865,381; 8,952,801; 8,546,140; 9,644,184; 9,328,332; and 8,765,470, each of which is incorporated by reference in its entirety.
The second approach to reprogramming TiPSC involves identification of specific T cells that carry specific TCR gene rearrangements which endow the encoded TCR with a known antigen and HLA specificity (FIG. 1 A). For example, T cells that recognize the influenza A antigenic peptide GILGFVFTL in the context of HLA-A*02:01 are collected, activated using mitogens and IL-2 and reprogrammed using methods known in the art. Exemplary methods of iPSC reprogramming are described in U.S. Pat. Nos. 8,183,038; 8,268,620; 8,440,461;
9,499,786; 10,865,381; 8,952,801; 8,546,140; 9,644,184; 9,328,332; and 8,765,470, each of which is incorporated by reference in its entirety. The resulting TiPSC is then used to derive T cells that express the original antigen-specific TCR.
Differentiating ab iT cell
For generation of HPC from ab T-PiPSC, iPSC were cultured in HDM basal medium, composed of 50% Iscove’s Modified Dulbecco’s Medium and 50% Ham’s F12 Nutrient Mixture supplemented with B-27 Supplement, XenoFree, minus Vitamin A (IX), Non-Essential Amino Acids (IX), L-Ascorbic Acid Phosphate Magnesium Salt n-Hydrate (250 uM), Monothioglycerol (100 uM), and Heparin (100 ng/ml). On Day 0, HDM basal medium was supplemented with HI 152 (1 uM), CHIR99021 (2 uM), bFGF (50 ng/ml), and VEGF (50 ng/ml). On Day 1, 80% of medium was removed and replaced with HDM basal medium supplemented with CHIR99021 (2 uM), bFGF (50 ng/ml), and VEGF (50 ng/ml). On Days 2, 3, and 4, 80% of medium was removed and replaced with HDM basal medium supplemented with BMP4 (25 ng/ml), bFGF (50 ng/ml), and VEGF (50 ng/ml). On Days 5, 6, 7, 8, 80% of medium was removed and replaced with HDM basal medium supplemented with BMP4 (5 ng/ml), SCF (100 ng/ml), TPO (50 ng/ml), FLT3L (20 ng/ml), and IL-3 (20 ng/ml). HPCs were harvested between days 7-9 depending on starting iPSC source. HPC were defined as CD34+, CD43+, +/- CD45 on the cell surface. The differentiation conditions for generation of alpha beta iPSC-derived T (ab iT) cells from ab T-HPCs are important, not only for optimal yield of iT cells having a TCR+ and CD3+ phenotype, but also for optimizing the function of the iT cell, including proliferation and target killing. In order to generate a superior ab iT cell, conditions were tested for improved yield, viability and phenotype, as well as fitness and target killing of the iT cell. Illustrated herein is an exemplary method of differentiation of a CD34+ HPC to iT cell, wherein the CD34+ cell expresses a rearranged TCR, including but not limited to, a trusted rearranged TCR.
Notch signaling, in particular, plays a key role in driving precursor cells towards a T cell fate. In the human thymus, the Notch family proteins DLL1, DLL4, and Jag2 (expressed by stromal cells in the thymus) signal through the receptor Notchl (expressed by early thymocytes). To test the effects of DLL4 and DLL4 with JAG2 on iT cell differentiation, HPCs were cultured on plates coated using the following proteins for 21 to 35 days: recombinant Delta-like protein 4 (DLL4) with Retronectin® (Takara Bio, Shiga, Japan) and DLL4 with recombinant Jagged 2 (JAG2) and Retronectin®. T cell differentiation medium (TCDM) basal medium used to differentiate HPCs to iT cells was composed of CTS AIM V Medium supplemented with CTS Immune Cell Serum Replacement (10%), Glutamax Supplement (IX), L- Ascorbic Acid Phosphate Magnesium Salt n-Hydrate (250 uM), and Nicotinamide (2 mM). FIG. 2 demonstrates that the combination of DLL4 and JAG2 increased the yield of iT cells.
The addition of cytokines in Days 14-28 of differentiation was also assessed. TCDM basal medium was supplemented with IL-2 and IL-7, with and without IL-15. The addition of IL- 15 in the medium increased the yield of iT cells as well as the % viable iT cells at Day 28 (FIG. 3). To further test the function of iT cells treated with IL-15 and DLL4 or DLL4 and JAG2,
HPCs were generated from iPSCs engineered to express a CD 19-targeting CAR and cultured as described above. Amongst cells treated with IL-15, those cultured on DLL4 and JAG2 coated plates had increased iT cell viability and an increase in lysis of CD19+ Reh target cells (FIG. 4).
Differentiation conditions were next tested to optimize the TCR avidity in the resultant iT cell. In days 21-28 of differentiation, cells were cultured on plates coated with one of two anti- CD3 antibodies, OKT3 (Rung et ah, Science. 1979 Oct 19;206(4416): 347-9) or UCHT1 (Callard et al., Clin Exp Immunol. 1981 Mar;43(3):497-505). Both antibodies target overlapping epitope but demonstrate different effects (e.g. inducing confirmational changes to CD3/TCR, strength of agonism, etc.). When comparing OKT3 and UCHT1, UCHT1 supported more faithful T cell identity (TCR/CD3+) whereas 0KT3 elicited more CD56 expression (data not shown). When the antibodies were compared amongst cells treated with IL-15, UCHT1 resulted in higher iT yield as well as increased lysis of CD 19+ target cells (FIG. 5).
Through testing of varying conditions at multiple time points, the following improved differentiation method was discovered which yields iT cells with superior viability and function. HPC cells were thawed and CD34+ cells enriched using MicroBead Kit. CD34+ cells were seeded at 2.5E4 viable cells/cm2 on DLL4/JAG2/RN (Retronectin®, a recombinant human fibronectin fragment) coated plates in TCDM-I medium. TCDM-I is TCDM basal medium supplemented with SCF (50 ng/ml), FLT3L (50 ng/ml), TPO (50 ng/ml), and IL-7 (50 ng/ml). Cells were collected weekly and re-seeded on protein coated plates from days 1-14. At day 14 cells were cryopreserved. Cryopreserved cells were then thawed and seeded on DLL4/JAG2/RN coated plates in TCDM-I medium at 4.16E4 viable cells/cm2. Medium was changed every 24-72 hours using TCDM-I medium from days 14-21. At day 21, cells were collected and seeded at 8.3E4 viable cells/cm2 on UCHT1 anti-CD3 Ab (2 ug/ml) admixed with MOPC-21 mouse IgG Isotype Ab (Melchers, Biochem J. 1970 Oct;l 19(4):765-72) (8 ug/ml) coated plates in TCDM + IL-2, IL-7, IL-15. At day 28 cells were collected for evaluation (FIG 6).
Example 2. Generating CAR-ab T cells
A T-iPSC line that was derived from an ab T cell expressing a TCR having unknown- specificity were engineered to express a CD 19-targeting CAR to evaluate their tumor cell killing activity. The CAR-T-iPSC cells were used to differentiate ab T cells using the method described in Example 1. After 28 days of differentiation, cells were collected and stained for lineage markers, maturation markers and cytokine receptors, and then analyzed by flow cytometry (FIG. 7). The majority of cells were CD45-positive. CD45-expressing cells were analyzed for all other markers. The CD45-positive cells co-expressed TCRo$ and CD3. Most of the CD3-positive cells are CD56-negative. The majority of cells expressed CD7 with a subset positive for both CD7 and CD5. When CD8 was expressed, it was as a heterodimer of CD8a and Eϋ8b. No CD4 expression was detected. Expression of co-stimulatory molecules CD28 and CD27 was low.
Cells expressed IL-2 family cytokine receptors including CD25, CD122, CD127, CD132 and CD215. Further, Day 28 CAR-iT cells were left unstained or stained with anti-FMC63 CAR antibody. Most (74%) of the CAR-iT cells expressed the CAR protein on their surface (FIG. 8). The CAR-iT cells were then assessed for antigen-specific killing of B cell lymphoma cells (Reh). For these studies, either Reh cells or a version of Reh cells where the CD19 gene was knocked out to make CD19-negative cells were used. Either CAR-iT cells or PBMC-derived CART cells were co-cultured at a 1:1 ratio with target cells. Target cell killing was measured using an IncuCyte instrument. When CD 19-positive Reh cells were exposed to CAR-T cells, both iPSC-derived and PBMC-derived CAR-iT cells mediated tumor killing (FIG. 9A). By contrast, CD 19-negative Reh targets were spared from killing (FIG. 9B).
Example 3. Identifying Trusted TCRs
Public TCRs are those sequences that occur frequently in multiple individuals with a certain HLA type. For example, there are public TCRs that recognize an antigenic peptide sequence of the influenza A virus matrix protein (epitope: GILGFVFTL) in the context of the HLA-I molecule HLA-A*02:01. Most, if not all, people who carry the HLA-A*02:01 allele and who have been exposed to influenza A will also have T cells that share a common public TCR. The homology of such public TCRs can be described at two levels. At the gene level, these public TCRs share TCR alpha V (TRAV) and TCR beta V (TRBV) gene use, however they might differ at the sequence level as a consequence of random n/p nucleotide additions during TCR rearrangement or by use of different diversity (TRBV/TRAV) or joining (TRBJ) genes (FIG. 10). Such public TCRs will be referred to herein as public TCR allotypes. The physical intersection of rearranged V gene, D gene and J gene (beta chain) or V gene and J gene (alpha chain) along with n/p additions, comprises the part of the TCR that confers specificity for an antigen - the so-called complementarity determining region 3 (CDR3). Table 3. Example of public TCR types bases on differing levels of identity
Figure imgf000087_0001
Those individuals who carry HLA-A*02:01 will also carry a second HLA-A gene (usually not HLA-A*02:01), two HLA-B genes, and two HLA-C genes, and because those other genes are diverse between individuals, the public TCR allotypes and sequences have been de- risked in nature (FIG. 11). That is, these TCRs are exposed to a vast diversity of other non-HLA- A*02 proteins during thymic selection and they are not purged. Thus, these TCRs fail to recognize non-HLA-A*02 molecules and are unlikely to participate in graft versus host disease, even in people who lack HLA-A*02:01.
PiPSCs were engineered to express a recombinant public rearranged ab TCR having an alpha chain of SEQ ID NO: 84 and a beta chain of SEQ ID NO: 85 according to the method shown in FIG. IB. The recombinant public rearranged ab TCR recognizes the influenza epitope GILGFVFTL (SEQ ID NO: 83) in the context of HLA-A* 02:01. The transgene was under control of a constitutive CAG promoter. Nalm6 cells, a B cell precursor leukemia cell line, engineered to express a negative control or GILGFVFTL epitope were cultured with the engineered ab iT cells at a 1 : 1 or 5: 1 effector to target ratio. FIG. 12 shows that ab iT cells engineered to express the public TCR were able to kill target cells expressing the flu epitope, demonstrating that the genomic engineered public TCR was functional.
It will be appreciated by those skilled in the art that changes could be made to the embodiments described above without departing from the broad inventive concept thereof. It is understood, therefore, that this invention is not limited to the particular embodiments disclosed, but it is intended to cover modifications within the spirit and scope of the present invention as defined by the present description.

Claims

CLAIMS claimed:
1. An induced pluripotent stem cell (iPSC) comprising:
(i) one or more polynucleotides encoding a recombinant rearranged ab T cell receptor (TCR); and
(ii) a polynucleotide encoding a chimeric antigen receptor (CAR), wherein the rearranged ab TCR is a public TCR that specifically recognizes a non human antigen in the context of a specific HLA class I (HLA-I) allele and wherein the rearranged ab TCR supports differentiation of the iPSC to a T cell.
2. The iPSC according to claim 1, wherein the rearranged ab TCR enables expansion of the T cell differentiated from the iPSC after mitogenic stimulation.
3. The iPSC according to claim 1, wherein the one or more polynucleotides encoding the recombinant rearranged ab TCR comprise an a TCR variable gene selected from the group consisting of TRAV27 and TRAV13-1; an a TCRjoining gene selected from the group consisting of TRAJ41 and TRAJ37; and an a TCR constant gene TRAC.
4. The iPSC according to any one of claims 1-3, wherein the one or more polynucleotides encoding the recombinant rearranged ab TCR comprise a b chain variable gene TRBV19; a b chain variable gene selected from the group consisting of TRBJ2-7, TRBJ2-5, and TRBJ2-6; or a b chain constant gene selected from the group consisting of TRBCl and TRBC2.
5. The iPSC according to any one of claims 1-4, wherein the recombinant rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
6. The iPSC according to any one of claims 1-5, wherein the iPSC is reprogrammed from peripheral blood mononuclear cells (PBMCs), preferably CD34+ hematopoietic stem cells (HSCs) or ab T cells.
7. A T cell derived from the iPSC according to any one of claims 1-6.
8. An induced pluripotent stem cell (iPSC) or a T cell derived therefrom comprising: one or more polynucleotides encoding a rearranged ab T cell receptor (TCR), wherein the rearranged ab TCR is a public TCR that specifically recognizes a non-human antigen in the context of a specific HLA class I allele (HLA-I) and the rearranged ab TCR supports differentiation of the iPSC to the T cell, and an exogenous polynucleotide encoding a chimeric antigen receptor (CAR); and one or more of the following additional features:
(a) an exogenous polynucleotide encoding an artificial cell death polypeptide;
(b) a deletion or reduced expression of one or more of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CUT A, RFX5 and RFXAP genes;
(c) a deletion or reduced expression of RAG1 and RAG2 genes;
(d) an exogenous polynucleotide encoding a non-naturally occurring variant of FcyRIII (CD 16);
(e) an exogenous polynucleotide encoding interleukin 15 (IL-15) and/or IL-15 receptor or a variant or truncation thereof;
(f) an exogeneous polynucleotide encoding a constitutively active interleukin 7 (IL- 7) receptor or variant thereof;
(g) an exogenous polynucleotide encoding interleukin 12 (IL-12) or interleukin 21 (IL- 21) or a variant thereof;
(h) an exogenous polynucleotide encoding human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G);
(i) an exogenous polynucleotide encoding leukocyte surface antigen cluster of differentiation CD47 (CD47) and/or CD24; or an exogenous polynucleotide encoding one or more imaging or reporter proteins, such as PSMA or HSV-tk.
9. The iPSC or T cell according to claim 8, wherein the rearranged ab TCR enables increased expansion of the T cell differentiated from the iPSC after mitogenic stimulation than a T cell without the rearranged ab TCR.
10. The iPSC or T cell according to claim 8, wherein the iPSC is reprogrammed from an ab T cell and the rearranged ab TCR is endogenous to the ab T cell.
11. The iPSC or T cell according to claim 8, wherein the rearranged ab TCR is recombinant.
12. The iPSC or T cell according to claim 11, wherein the iPSC is reprogrammed from peripheral blood mononuclear cells (PBMCs), preferably CD34+ hematopoietic stem cells (HSCs) or ab T cells.
13. The iPSC or T cell according to any one of claims 8-12, wherein the rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
14. The iPSC or T cell according to any one of claims 8-13, comprising an exogenous polynucleotide encoding a human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G).
15. The iPSC or T cell according to any one of claims 8-14, wherein one or more of the exogenous polynucleotides are integrated at one or more loci on the chromosome of the cell selected from the group consisting of AAVS1, CCR5, ROSA26, collagen, HTRP, HI 1, GAPDH, RUNX1, B2M, TAPI, TAP2, Tapasin, NLRC5, CUT A, RFXANK, CUT A, RFX5, RFXAP, TRAC, TRBCl, TRBC2, RAG1, RAG2, NKG2A, NKG2D, CD38, CIS, CBL-B, SOCS2, PD1, CTLA4, LAG3, TIM3, or TIGIT genes, provided at least one of the exogenous polynucleotides is integrated at a locus of a gene selected from the group consisting of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CIITA, RFX5 and RFXAP genes to thereby result in a deletion or reduced expression of the gene.
16. The iPSC or T cell according to claim 15, wherein one or more of the exogenous polynucleotides are integrated at the loci of the CIITA, AAVS1 and B2M genes.
17. The iPSC or T cell according to claim 16, having a deletion or reduced expression of one or more of B2M or CIITA genes.
18. The iPSC or T cell according to any one of claims 1-17, wherein the rearranged ab TCR comprises an a TCR chain having a CDR3 of the amino acid sequence of SEQ ID NO: 84, and a b TCR chain having a CDR3 of the amino acid sequence of SEQ ID NO: 85.
19. The iPSC or T cell according to any one of claims 18, wherein the ab TCR comprises an a TCR chain comprising the amino acid sequence encoded by TRAV27 and TRAJ41 genes, and having the CDR3 of the amino acid sequence of SEQ ID NO: 84, and the b TCR chain comprising the amino acid sequence encoded by TRBV19 and TRBJ2-7 genes, and having the CDR3 of the amino acid sequence of SEQ ID NO: 85.
20. The iPSC or T cell according to any one of claims 1-19, wherein the CAR comprises:
(i) a signal peptide comprising a signal peptide;
(ii) an extracellular domain comprising a binding domain that specifically binds an antigen on a target cell;
(iii) a hinge region;
(iv) a transmembrane domain;
(v) an intracellular signaling domain; and
(vi) a co-stimulatory domain.
21. The iPSC or T cell according to claim 20, wherein the signal peptide is GMCSF signal peptide.
22. The iPSC or T cell according to claim 20, wherein the extracellular domain comprises an scFv or VHH derived from an antibody that specifically binds an antigen that is expressed on cancer cells.
23. The iPSC or T cell according to claim 20, wherein the hinge region comprises a CD28 hinge region, a CD8 hinge region, or an IgG hinge region.
24. The iPSC or T cell according to claim 20, wherein the transmembrane domain comprises a CD28 transmembrane domain or a CD8 transmembrane domain.
25. The iPSC or T cell according to claim 20, wherein the intracellular signaling domain is derived from DAP10, DAP12, Fc epsilon receptor I g chain (FCER1G), FcR b, NKG2D, CD35, CD3 , CD3y, CD3z, CD5, CD22, CD226, CD66d, CD79A, or CD79B.
26. The iPSC or T cell according to claim 20, wherein the co-stimulatory domain is a co stimulatory signaling domains are derived from CD28, 4 IBB, IL2Rb, CD40, 0X40 (CD 134), CD80, CD86, CD27, ICOS, NKG2D, DAP10, DAP 12, or 2B4 (CD244).
27. The iPSC or T cell according to claim 20, wherein the CAR comprises:
(i) the signal peptide comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 1;
(ii) the extracellular domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 7; (iii) the hinge region comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 22;
(iv) the transmembrane domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 24;
(v) the intracellular signaling domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 6; and
(vi) the co-stimulatory domain comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 20.
28. The iPSC or T cell according to claim 20, wherein the CAR comprises:
(i) the signal peptide comprising the amino acid sequence of SEQ ID NO: 1;
(ii) the extracellular domain comprising the amino acid sequence of SEQ ID NO: 7;
(iii) the hinge region comprising an amino acid sequence of SEQ ID NO: 22;
(iv) the transmembrane domain comprising the amino acid sequence of SEQ ID NO: 24;
(v) the intracellular signaling domain comprising the amino acid sequence of SEQ ID NO: 6; and
(vi) the co-stimulatory domain comprising the amino acid sequence of SEQ ID NO: 20
29. The iPSC or T cell according to any one of claims 8-28, wherein the mechanism of action of the artificial cell death polypeptide is metabolic, dimerization-inducing or therapeutic monoclonal antibody-mediated.
30. The iPSC or T cell according to claim 29, wherein the therapeutic monoclonal antibody mediated artificial cell death polypeptide is an inactivated cell surface protein selected from the group of monoclonal antibody specific epitopes selected from epitopes specifically recognized by ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, polatuzumab vedotin, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimumab, belimumab, canakinumab, denosumab, golimumab, ipilimumab, ofatumumab, panitumumab, or ustekinumab.
31. The iPSC or T cell according to claim 30, wherein the inactivated cell surface protein is a truncated epithelial growth factor (tEGFR) variant.
32. The iPSC or T cell according to claim 31, wherein the tEGFR variant consists of an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 71.
33. The iPSC or T cell according to claim 14, wherein the HLA-E comprises an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 66 or the HLA-G comprises an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 69.
34. The iPSC or the T cell according to any one of claims 14-33, wherein:
(i) the exogenous polynucleotide encoding the chimeric antigen receptor (CAR) is integrated at a locus of AAVS1 gene;
(ii) the exogenous polypeptide encoding the artificial cell death polypeptide is integrated at a locus of CIITA gene; and (iii) the exogenous polypeptide encoding the human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G) is integrated at a locus of B2M gene; wherein integration of the exogenous polynucleotides deletes or reduces expression of CIITA and B2M.
35. An induced pluripotent stem cell (iPSC) or a T cell comprising: (i) an exogenous polynucleotide encoding a chimeric antigen receptor (CAR) having the amino acid sequence of SEQ ID NO: 61;
(ii) an exogenous polynucleotide encoding an artificial cell death polypeptide comprising an apoptosis-inducing domain having the amino acid sequence of SEQ ID NO: 71; (iii) a polynucleotide encoding a rearranged T cell receptor (TCR) locus comprising an a TCR having the amino acid sequence of SEQ ID NO: 86, and a b TCR having the amino acid sequence of SEQ ID NO: 87; and
(iv) optionally, an exogenous polynucleotide encoding a human leukocyte antigen E (HLA-E) having the amino acid sequence of SEQ ID NO: 66; wherein one or more of the exogenous polynucleotides are integrated at loci of AAVS1, CIITA and B2M genes, to thereby delete or reduce expression of CIITA and B2M.
36. A composition comprising the T cell according to any one of the claims 7-35.
37. The composition according to claim 36, further comprising or being used in combination with, one or more therapeutic agents selected from the group consisting of a peptide, a cytokine, a checkpoint inhibitor, a mitogen, a growth factor, a small RNA, a dsRNA (double stranded RNA), siRNA, oligonucleotide, mononuclear blood cells, a vector comprising one or more polynucleic acids of interest, an antibody, a chemotherapeutic agent or a radioactive moiety, or an immunomodulatory drug (IMiD).
38. A method of treating cancer in a subject in need thereof, comprising administering the cell according to any one of claims 1-35 or the composition according to any one of claims 36 and 37 to the subject in need thereof.
39. The method according to claim 38, wherein the cancer is non-Hodgkin’s lymphoma (NHL).
40. A method of manufacturing a T cell comprising differentiating an iPSC cell according to any one of claims 1-35 under conditions for cell differentiation to thereby obtain the T cell.
41. The method according to claim 40, wherein the iPSC is obtained by genomic engineering the iPSC, wherein the genomic engineering comprises targeted editing.
42. The method according to claim 41, wherein the targeted editing comprises deletion, insertion, or in/del carried out by CRISPR, ZFN, TALEN, homing nuclease, homology recombination, or any other functional variation of these methods.
43. A CD34+ hematopoietic progenitor cell (HPC) derived from an induced pluripotent stem cell (iPSC) comprising one or more polynucleotides encoding a rearranged ab T cell receptor (TCR), wherein the rearranged ab TCR is a public TCR that specifically recognizes a non-human antigen in the context of a specific HLA class I (HLA-I) allele and the rearranged ab TCR supports differentiation of the iPSC to a T cell, and an exogenous polynucleotide encoding a chimeric antigen receptor (CAR); and one or more of the following additional features:
(a) an exogenous polynucleotide encoding an artificial cell death polypeptide;
(b) a deletion or reduced expression of one or more of B2M, TAP 1, TAP 2, Tapasin, RFXANK, CUT A, RFX5 and RFXAP genes;
(c) a deletion or reduced expression of RAG1 and RAG2 genes;
(d) an exogenous polynucleotide encoding a non-naturally occurring variant of FcyRIII (CD 16);
(e) an exogenous polynucleotide encoding interleukin 15 (IL-15) and/or interleukin (EL-15) receptor or a variant or truncation thereof;
(f) an exogeneous polynucleotide encoding a constitutively active interleukin 7 (IL-7) receptor or variant thereof;
(g) an exogenous polynucleotide encoding interleukin 12 (IL-12) or interleukin 21 (IL- 21) or a variant thereof;
(h) an exogenous polynucleotide encoding human leukocyte antigen E (HLA-E) and/or human leukocyte antigen G (HLA-G);
(i) an exogenous polynucleotide encoding leukocyte surface antigen cluster of differentiation CD47 (CD47) and/or CD24; or an exogenous polynucleotide encoding one or more imaging or reporter proteins, such as PSMA or HSV-tk.
44. The CD34+ HPC according to claim 43, wherein the iPSC is reprogrammed from whole peripheral blood mononuclear cells (PBMCs).
45. The CD34+ HPC according to claim 44, wherein the rearranged ab TCR enables increased expansion of the T cell differentiated from the iPSC after mitogenic stimulation than a T cell without the rearranged ab TCR.
46. The CD34+ HPC according to claim 43, wherein the iPSC is reprogrammed from an ab T cell and the rearranged ab TCR is endogenous to the ab T cell.
47. The CD34+ HPC according to claim 43, wherein the rearranged ab TCR is recombinant.
48. The CD34+ HPC according to any one of claims 43-47, wherein the rearranged ab TCR binds to an antigen derived from a virus, wherein the virus is selected from the group consisting of influenza-A, Epstein-Barr virus (EBV), and Cytomegalovirus (CMV).
49. A method of differentiating a CD34+ hematopoietic progenitor cell (HPC) comprising a polynucleotide encoding a rearranged TCR, such as an induced-pluripotent stem cell (iPSC)-derived CD34+ HPC, to a T cell, the method comprising culturing the CD34+ HPC in a medium comprising Delta-like protein 4 (DLL4) and Jagged 2 (JAG2), optionally further comprising a fibronectin protein or fragment thereof, SCF, induced- pluripotent stem cell (iPSC)-derived FLT3L, TPO, and/or IL-7.
50. The method according to claim 49, wherein the DLL4 and JAG2 proteins are immobilized on a cell culture plate, such as by using polydopamine in the presence or absence of Protein G coating.
51. The method according to claim 49 or 50, wherein the cells are cultured in the medium comprising DLL4 and JAG2 for about 21 to about 35 days.
52. The method according to any one of claims 49-51, further comprising culturing the cells in a medium comprising one or more cytokines selected from the group consisting of interleukin-2 (IL-2), IL-7, and IL-15.
53. The method according to any one of claims 49-52, further comprising culturing cells in a medium comprising an anti-CD3 antibody, preferably the anti-CD3 antibody is OKT3 or UCHT1.
54. A method of differentiating an induced-pluripotent stem cell (iPSC)-derived CD34+ hematopoietic progenitor cell (HPC) comprising a polynucleotide encoding a rearranged TCR to a T cell, the method comprising:
(a) culturing the cell in a medium comprising recombinant Delta-like protein 4 (DLL4) and recombinant Jagged 2 (JAG2), optionally further comprising a fibronectin protein or fragment thereof, SCF, FLT3L, TPO, and/or IL-7;
(b) culturing the cell in a medium comprising interleukin-2 (IL-2), IL-7, and IL-15; and (c) culturing the cell in a medium comprising an anti-CD3 antibody, preferably OKT3 or UCHTl.
55. The method according to any one of claims 49-54, wherein the cell is cultured in the medium comprising recombinant DLL4 and JAG2 from day 0 to about day 21 of differentiation.
56. The method according to any one of claims 54 or 55, wherein the cell is cultured in the medium comprising IL-2, IL-7, and IL-15 from day 21 to about day 28 of differentiation.
57. The method according to any one of claims 54 to 56, wherein the cell is cultured in the medium the anti-CD3 antibody from day 21 to about day 28 of differentiation.
58. A recombinant Delta-like protein 4 (DLL4) variant polypeptide having an amino acid comprising an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to SEQ ID NO: 90.
59. A method of differentiating an induced-pluripotent stem cell (iPSC)-derived CD34+ hematopoietic progenitor cell (HPC) comprising a polynucleotide encoding a rearranged TCR to a T cell, the method comprising culturing the CD34+ HPC in a medium comprising a recombinant DLL4 variant according to claim 58.
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